chilledchaosofficial
wsswatson:

Another three episodes. Another series finished. Another set of surprises. Another cliffhanger.
As is to be expected, fans have been going wild, theories have been spreading like wildfire, and conversation is roaring.
I have a few theories of my own, and after a few rewatches, I’m ready to lay them all out. I’m going to try to lay them out chronologically so that you can consider them as and when you rewatch the episode, but some jumping about will be necessary.
So, here we go:
THESES: The woman we know as Mary Morstan was in cahoots with Moriarty. Sherlock was lying about trusting her. Mycroft saved Sherlock’s life.
Mary first.
Let’s have a think about the scene in which Mary shoots Sherlock. The first thing that leaped out at me was her clothing. Mary is dressed in the clothing of an assassin. People have been arguing that Mary has changed and left that life behind her. Has she really? She kept the clothes, and the gun. She kept them hidden from John, too. Even if she’s no longer ‘in business’, she hasn’t retired, either.
Now, let’s take a look at the shooting itself. Just before it takes place, the following dialogue occurs:
SHERLOCK: “Mary, whatever he’s got on you, let me help.”
MARY: “Oh, Sherlock, if you take one more step, I swear I will kill you.”
SHERLOCK: “No, Mrs Watson.* You won’t.”
*An appeal to Mary’s sentiment by referencing their shared connection to John?
Then, of course, she shoots him, and notice the look of surprise on Sherlock’s face:

His last word before he falls unconscious is “Mary?”
He was not expecting that, which supports my theory that she really did shoot to kill (bear with me).
Sherlock, in an attempt to save himself, enters his mind palace, where one of the first things that the Molly of his imagination says is: “You’re almost certainly going to die, so we need to focus.”
Then we have Mycroft: “It’s all very well having a mind palace, but you’ve only three seconds of consciousness left to use it.”
Then Mycroft says “What was directly behind you when you were murdered?”
Sherlock says “I haven’t been murdered yet!” to which Mycroft replies “Balance of probability, little brother.”
Now, remember that Molly and Mycroft are not really present - all of this takes place in Sherlock’s head. Conclusion? Sherlock thinks that Mary shot to kill.
She succeeded, too. His heart stopped. The surgeons moved away, they gave up. Sherlock died.
What saved him?
John arrived and spoke to him.
Then Moriarty, in Sherlock’s mind palace, said “…And John will cry buckets and buckets. It’s him I worry about the most. That wife! You’re letting him down, Sherlock. John Watson is definitely in danger.”
Again, remember that Moriarty is not really the one speaking. This is all in Sherlock’s head. Sherlock fought his way back to life because he believed John to be in danger from Mary. Sherlock does not trust Mary, and he certainly doesn’t trust her with his best friend.
Then there’s what John said at the hospital: “His first word when he woke up? ‘Mary’!”
He woke up thinking of her. He definitely does not trust her.
Look how she reacts to hearing that he’s alright, too:

That is not a look of relief.
Then Mary visits him, and says: “You don’t tell him. Sherlock! You don’t tell John. … Look at me, and tell me you’re not going to tell him.”
If she was sorry, she would’ve said so. If she was sorry, there would have been at least a hint of remorse in her tone. There was not. Her tone was threatening. She didn’t ask him not to tell John, she told him, and by this point, we and Sherlock both know what she is capable of doing to people.
This is also proof of just how selfish Mary’s love for John is. When you love someone, really love them, your priority is their safety. Mary’s priority is not John’s safety - if she has such a dangerous past, the safest thing for John would be to come clean, because at some point, it’s possible that John might be targeted because of her (just as he has been because of Sherlock, and it was through Mary that Magnussen observed Sherlock’s reaction to John being placed in the fire).
It’s not “I’m sorry that I shot you. Even if I didn’t care about you one bit, I know that my husband does, and I am sorry to have caused him any pain through harming you.”
It’s “Don’t you dare tell my husband what I did, because then he will leave me.”
She loves John, certainly, but she is very, very selfish about it.
Of course, Sherlock’s still drowsy at that point. A little later, though, Janine visits, and just before she leaves, she says: “I’ll give your love to John and Mary.”
At this point, Sherlock’s face becomes determined, and he turns down the morphine tap. He gets ready to make his escape.
Cut to the mind palace, and look how Mary appears:

She’s dressed as she was the day she and Sherlock met. Which, by the way was suspicious in itself, as she appeared to have no idea who Sherlock was - “John? John, what is it? Oh, no, you’re- [Sherlock].” Sherlock was all over the papers. Everyone knew what he looked like, and someone so close to John certainly would. That implies to me that she knows more about him than she was willing to let on, and so pretended to know nothing at all. Liar.
Then look at how she reacts to discovering Sherlock’s ‘number 1 bolthole’:


That is a look of pure suspicion and trepidation. Not only does Sherlock not trust Mary, she doesn’t trust him either.
Now let’s talk about the dialogue back in 221b:
JOHN: “He knew who shot him. The bullet wound was here, so he was facing whoever it was.”
LESTRADE: “So why not tell us? Because he’s tracking them down himself-“
JOHN: “Or protecting them?”
LESTRADE: “Protecting the shooter - why?”
JOHN: “Protecting someone, then. But why would he care? He’s Sherlock. Who would he bother protecting?”
And this is the shot as he finishes speaking:

In this shot, if only very partially, is John, Lestrade and Mrs Hudson, the three people Sherlock risked his life to save when he jumped off the roof of Bart’s. If you want some subliminal messaging that Sherlock was not protecting the shooter, but, as John said, ‘someone’, there it is. At the center of the shot is John, who then, of course, comes to a realisation: he’s sitting in my armchair. He then asks:
"Mrs Hudson, why did Sherlock think I’d be moving back in here?"
The realisation hits him then. Sherlock was not protecting the shooter. He was protecting his best friend.
Let’s skip along a little bit. Mary goes to Leinster Gardens, where Sherlock calls her. He brings her to his bolthole. How does he describe that bolthole?
"The empty houses."
Let’s take a look at an extract from The Adventure of the Empty House:

I had imagined that we were bound for Baker Street, but Holmes stopped the cab at the corner of Cavendish Square. I observed that as he stepped out he gave a most searching glance to right and left, and at every subsequent street corner he took the utmost pains to assure that he was not followed. Our route was certainly a singular one. Holmes’s knowledge of the byways of London was extraordinary, and on this occasion he passed rapidly and with an assured step through a network of mews and stables, the very existence of which I had never known. We emerged at last into a small road, lined with old, gloomy houses, which led us into Manchester Street, and so to Blandford Street. Here he turned swiftly down a narrow passage, passed through a wooden gate into a deserted yard, and then opened with a key the back door of a house. We entered together, and he closed it behind us.
The place was pitch dark, but it was evident to me that it was an empty house. Our feet creaked and crackled over the bare planking, and my outstretched hand touched a wall from which the paper was hanging in ribbons. Holmes’s cold, thin fingers closed round my wrist and led me forward down a long hall, until I dimly saw the murky fanlight over the door. Here Holmes turned suddenly to the right, and we found ourselves in a large, square, empty room, heavily shadowed in the corners, but faintly lit in the centre from the lights of the street beyond. There was no lamp near, and the window was thick with dust, so that we could only just discern each other’s figures within. My companion put his hand upon my shoulder and his lips close to my ear.
“Do you know where we are?” he whispered.
“Surely that is Baker Street,” I answered, staring through the dim window.
“Exactly. We are in Camden House, which stands opposite to our own old quarters.”
“But why are we here?”
“Because it commands so excellent a view of that picturesque pile. Might I trouble you, my dear Watson, to draw a little nearer to the window, taking every precaution not to show yourself, and then to look up at our old rooms–the starting-point of so many of your little fairy-tales? We will see if my three years of absence have entirely taken away my power to surprise you.”
I crept forward and looked across at the familiar window. As my eyes fell upon it, I gave a gasp and a cry of amazement. The blind was down, and a strong light was burning in the room. The shadow of a man who was seated in a chair within was thrown in hard, black outline upon the luminous screen of the window. There was no mistaking the poise of the head, the squareness of the shoulders, the sharpness of the features. The face was turned half-round, and the effect was that of one of those black silhouettes which our grandparents loved to frame. It was a perfect reproduction of Holmes. So amazed was I that I threw out my hand to make sure that the man himself was standing beside me. He was quivering with silent laughter.
“Well?” said he.
“Good heavens!” I cried. “It is marvellous.”
“I trust that age doth not wither nor custom stale my infinite variety,” said he, and I recognized in his voice the joy and pride which the artist takes in his own creation. “It really is rather like me, is it not?”
“I should be prepared to swear that it was you.”
“The credit of the execution is due to Monsieur Oscar Meunier, of Grenoble, who spent some days in doing the moulding. It is a bust in wax. The rest I arranged myself during my visit to Baker Street this afternoon.”
“But why?”
“Because, my dear Watson, I had the strongest possible reason for wishing certain people to think that I was there when I was really elsewhere.”
“And you thought the rooms were watched?”
“I knew that they were watched.”
“By whom?”
“By my old enemies, Watson. By the charming society whose leader lies in the Reichenbach Fall. You must remember that they knew, and only they knew, that I was still alive. Sooner or later they believed that I should come back to my rooms. They watched them continuously, and this morning they saw me arrive.”

The specific enemy in question, who Holmes and Watson apprehend, is Colonel Sebastian Moran, the late Moriarty’s right-hand man, described thus:

Moran, Sebastian, Colonel. Unemployed. Formerly 1st Bangalore Pioneers. Born London, 1840. Son of Sir Augustus Moran, C. B., once British Minister to Persia. Educated Eton and Oxford. Served in Jowaki Campaign, Afghan Campaign, Charasiab (despatches), Sherpur, and Cabul. Author of Heavy Game of the Western Himalayas (1881); Three Months in the Jungle (1884). Address: Conduit Street. Clubs: The Anglo-Indian, the Tankerville, the Bagatelle Card Club.
On the margin was written, in Holmes’s precise hand:
The second most dangerous man in London.

A trained assassin, currently unemployed, who Holmes and Watson confront in an empty house. Remind you of anyone?
Let’s add to that her very suspicious behaviour regarding apparently not recognising Sherlock on the day they met. May she, like Moran, have known that Sherlock was alive, and have been watching him?
Here, again, Sherlock demonstrates that he does not trust Mary: “Remind you of anyone, Mary? A façade?”
His later demonstration of apparent trust is most certainly an act.
Almost as soon as Mary enters the building, her hand goes to her gun:

She certainly doesn’t have any qualms with killing Sherlock. She confirms this herself not long afterwards:
MARY: “You were very slow.”
SHERLOCK: “How good a shot are you?”
MARY: “How badly d’you wanna find out?”
Now, of course she doesn’t then actually kill him - that would ruin the narrative; the shooting of the coin has to serve as a suitable alternative. She of course shoots it excellently. Now, here comes the odd bit:
SHERLOCK: “And yet over a distance of six feet you failed to make a kill shot. That wasn’t a miss. It was surgery. I’ll take the case.”
And yet, it wasn’t a miss. It was a very good shot. Sherlock died. So why say it? I’ll come back to that.
MARY: “What case?”
SHERLOCK: “Yours. Why didn’t you come to me in the first place?”
MARY: “Because John can’t ever know that I lied to him. It would break him and I would lose him forever, and Sherlock, I will never let that happen. Please, understand, there is nothing in this world I would not do to stop that happening.”
Like killing one of the most intelligent and observant men in the world who also happens to be his best friend, for instance? Your selfishness is showing again there, Mary.
Now let’s take a look at the confrontation between Sherlock, John and Mary back in 221b:
JOHN: “You… What have I ever done? Hm? My whole life… to deserve you.”
SHERLOCK: “Everything.”
JOHN: “Sherlock, I’ve told you… Shut up.”
SHERLOCK: “No, I mean it, seriously, everything. Everything you’ve ever done is what you did.”
JOHN: “Sherlock, one more word and you will not need morphine.”
SHERLOCK: “You’re a doctor who went to war; you’re a man who couldn’t stay in the suburbs for more than a month without storming a crack den, beating up a junkie. Your best friend is a sociopath who solves crimes as an alternative to getting high. That’s me by the way - hello! Even the landlady used to run a drug cartel. […] John, you are addicted to a certain lifestyle. You’re abnormally attracted to dangerous situations and people. So is it truly such a surprise that the woman you fall in love with conforms to that pattern?”
JOHN: “But she wasn’t supposed to be like that! Why is she like that?”
SHERLOCK: “Because you chose her.”
At first, this seems cruel. It seems as though Sherlock is forcing the blame of the situation on John, and certainly, that’s how John takes it - “Why is everything… always… MY FAULT?”
However, might this not be more evidence for the Mary-as-Moriarty’s-ex-right-hand-(wo)man theory? She’s not dangerous because John chose her or vice versa, but she put herself in John’s path because he’s caught up in that dangerous lifestyle, and with Sherlock.
She is, after all, a nurse, and does that suit her? Presumably she’s taken innocent lives. If she had only taken the lives of bad people, why would John care? He’s done exactly the same, as she presumably knows - he was, after all, in the army in a protective role. Mary is not an altruist. She does not have a personality suited to nursing. She presumably trained as a nurse during her five years since taking Mary Morstan’s identity, too, and not an NHS nurse, either - she works privately at John’s clinic. Less background checks, then. It seems to me that Mary intentionally put herself in John’s path. The Moriarty connection is looking likelier and likelier.
Let’s go a bit further.
SHERLOCK: “John, listen, be calm and answer me. What is she?”
JOHN: “My lying wife.”
SHERLOCK: “No, what is she?”
JOHN: “And the woman who is carrying my child who has lied to me since the day I met her.”
SHERLOCK: “No. Not in this flat, not in this room, right here, right now, what is she?”
JOHN: “Okay. Your way. Always your way. Sit.”
MARY: “Why?”
JOHN: “Because that’s where they sit! The people who come in here with their stories. The clients - that’s all you are now, Mary. You’re a client. This is where you sit and talk and this is where we sit and listen. Then we decide if we want you or not.”
In this scene, John completely places his trust in Sherlock and disowns Mary. He also mentions that she is carrying his child. Let’s continue.
Mary hands John a memory stick:

SHERLOCK: “A.G.R.A. What’s that?”
MARY: “My initials. Everything about who I was is on there.”
Oh, really? You said you would do anything to prevent John from finding out the truth about you, and yet you just happened to be carrying all of the information about your past with you?
Liar.
For those of you who aren’t away, the initials are a reference to a Great Agra Treasure of The Sign of Four, which turns out to be missing, the case empty:

“That is all over,” I answered. “It was nothing. I will tell you no more gloomy details. Let us turn to something brighter. There is the treasure. What could be brighter than that? I got leave to bring it with me, thinking that it would interest you to be the first to see it.”
“It would be of the greatest interest to me,” she said. There was no eagerness in her voice, however. It had struck her, doubtless, that it might seem ungracious upon her part to be indifferent to a prize which had cost so much to win.
“What a pretty box!” she said, stooping over it. “This is Indian work, I suppose?”
“Yes; it is Benares metal-work.”
“And so heavy!” she exclaimed, trying to raise it. “The box alone must be of some value. Where is the key?”
“Small threw it into the Thames,” I answered. “I must borrow Mrs. Forrester’s poker.”
There was in the front a thick and broad hasp, wrought in the image of a sitting Buddha. Under this I thrust the end of the poker and twisted it outward as a lever. The hasp sprang open with a loud snap. With trembling fingers I flung back the lid. We both stood gazing in astonishment. The box was empty!
No wonder that it was heavy. The ironwork was two-thirds of an inch thick all round. It was massive, well made, and solid, like a chest constructed to carry things of great price, but not one shred or crumb of metal or jewellery lay within it. It was absolutely and completely empty.
“The treasure is lost,” said Miss Morstan calmly.

I don’t think that that memory stick contained the truth, the whole truth and nothing but the truth, do you?
Then let’s look at this speech of Sherlock’s:
"By your skill set, you are or were an intelligence agent. Your accent is currently English but I suspect you are not. You’re on the run from something. You’ve used your skills to disappear, Magnussen knows your secret, which is why you were going to kill him, and I assume you befriended Janine in order to get close to him.”
'Are' is not looking likely. Look what MI6 has to say about that role:
'What about secrecy? Well obviously the details of your work will be secret and we ask you not to discuss your application with anybody. That said, once you join us you'll be able to disclose your role to one or two close friends or family. We'll help you create a credible cover story for everyone else.'
So why haven’t you disclosed your role to John, Mary? Where’s your credible cover story? No, she’s not an intelligence officer anymore.
She has disclosed her role to someone, though. Remember how quickly she said “Oh, he would have needed a confidante!” in reference to Sherlock going on the run? You’re on the run too, Mary. Who’s your confidante?
Then there’s this:
MARY: “The stuff Magnussen has on me - I would go to prison for the rest of my life.”
JOHN: “So you were just gonna kill him?”
MARY: “People like Magnussen should be killed, that’s why there are people like me.”
JOHN: “Perfect. So that’s what you were? An assassin? How could I not see that?”
MARY: “You did see that. And you married me. Because he’s right. It’s what you like.”
She’d go to prison for the rest of her life? Not if she was still with the secret service. She worked for much nastier people than that.
Here we also see another nasty trait of Mary’s come to light: she’s emotionally abusive. She turns the blame of the situation away from herself and onto John. She did say she’d do anything to prevent him from leaving her.
Look at John’s face, how he responds:

He is devastated, furious, he certainly doesn’t look like he plans to forgive her. So why do we see him do exactly that?
Well, for one thing, she’s carrying his child. He evidently cares about that - when she falls unconscious, he says to Sherlock: “Did you just drug my pregnant wife?” Emphasis on the ‘pregnant’.
For another, Sherlock tells him to: “John, John! Magnussen is all that matters now. You can trust Mary. She saved my life.”
Prior to that, he claimed that she fired “One precise shot to incapacitate [him] in the hope that it would give [her] time to negotiate [his] silence.” Yet again, she quite literally killed him. There is no proof that she really did call an ambulance, either - the scene in which we see her doing so is a reconstruction of Sherlock’s claim, and I used to have a horse. I saw lots of accidents. Multiple people would call an ambulance, and upon doing so, later people to call would be told that an ambulance had already been sent out to that particular incident. That didn’t happen to John. Perhaps there was good traffic that day, or an ambulance happened to be in the area. Besides, Sherlock fell unconscious within three seconds, went into shock (which can cause memory loss) and was dosed with morphine (which causes disorientation). Hardly the right circumstances to provide for a thorough analysis of the situation.
So why does Sherlock insist that Mary is trustworthy when he quite obviously doesn’t trust her? My guess is that he wants to placate her. He does, after all, say this in her presence. He wants to lull her into a sense of false security. We know that he wants what Magnussen has on her - “I want everything you’ve got on Mary”; “In return for the password, you will give me any material in your possession pertaining to the woman I know as Mary Watson” - but we don’t know why. Is it really to protect her? Or is it because he wants to know her secret?
John may be in on that - after all, he and Mary did undergo “months of silence”, and the timing of their ‘reconciliation’, just before the drugs took effect and everyone fell unconscious, was fortunate. I’m sure Sherlock invited John AND Mary to Christmas dinner for a reason. Perhaps John is just burdened by guilt and a sense of duty, and really is trying to forgive her, but the evidence suggests that he’s highly suspicious of her, too.
There’s also the fact that, when reconciling with her, he says “I’ve thought long and hard about what I want to say to you. These are prepared words, Mary. Chosen these words with care.” He also later says “I am very pissed off and it will come out now and then.”
John is not a good liar. Sherlock established this in The Empty Hearse:
JOHN: “One word, Sherlock, that is all I would’ve needed! One word to let me know that you were alive!”
SHERLOCK: “I’ve nearly been in contact so many times but I worried that, you know, you might say something indiscreet… You know, let the cat out of the bag.”
Now, nobody sounds natural when they speak from rehearsal. John’s repeated claim that that is what he’s doing, as well as letting Mary know that he will lose his temper with her in the future, is the perfect cover for an act by a not particularly good actor.
The editing of this section is important, too. It cuts between the confrontation scene in 221b and the reconciliation scene. That, to me, suggests that we are not supposed to buy into John’s forgiveness. It’s hard to, when we’ve just seen him so devastated and fuming.
So, onto the Magnussen scene. He really solidifies my theory that she was in cahoots with Moriarty. Let’s look at some of the things he says about her:
"I’m not a murderer, unlike your wife.”
'Murderer' is an interesting choice of word. It suggests worse than working with the secret service. If that was all he meant, presumably he would've said 'killer'. There are implications behind the word 'murderer' - implications of immorality.
"Oh, she’s bad, that one. So many dead people. You should see what I’ve seen."
Again, suggestions of immorality.
And my favourite:
"All those wet jobs for the CIA. Ooh! She’s gone a bit freelance now, bad girl. [laughter] Oh, she’s so wicked. I can really see why you like her.”
She clearly worked for someone who was not at all moral. Again, my bets are on Moriarty.
So why did Sherlock shoot Magnussen?
Well, let’s take a look at his expression upon discovering that Magnussen apparently keeps all of his blackmail material in his mind:

He looks horrified. Why? Because he cannot obtain the information and hence protect Mary? Or because he cannot obtain the information and hence learn her secret and hence protect John?
Then let’s consider what Magnussen says to John shortly before Sherlock shoots him:
"I know who Mary hurt and killed. I know where to find people who hate her. I know where they live. I know their phone numbers. All in my mind palace. I could phone them right now and tear your whole life down. And I will. Unless you let me flick your face."
After that, killing Magnussen seems to be Sherlock’s safest bet at protecting John. Mary may well be a risk to him, but so are all the people who hate her. John would be be fighting a war on two fronts if Magnussen set Mary’s enemies on her.
Then there’s the fact that Mycroft’s present (and in control). I think Sherlock suspects that Mycroft would protect him, and therefore allow him to continue to protect John. After all, as he said at the cottage: “Your loss would break my heart.” Indeed, he immediately commands: “Do not fire! Do not fire on Sherlock Holmes! Do not fire!”
In fact, I believe that Mycroft is the hero of this story.
Earlier on, at the cottage, he said to Sherlock:
"I have, by the way, a job offer I should like you to decline. […] MI6. They want to place you back into Eastern Europe. An undercover assignment that will prove fatal to you in, I think, about six months."
This is, of course, the assignment that Mycroft arranges for Sherlock to be sent on rather than being sent to prison for killing Magnussen. Now, would Mycroft do that without a plan? Would he really rather send Sherlock to his death than have him in prison? After all, “There will always come a time when we need Sherlock Holmes.”
Remember, too, how much Mycroft knows. He’s more intelligent than Sherlock, and Sherlock invited Mary to the family home when Mycroft was there. I suspect that Mycroft is well aware that something is up with Mary.
So, what does he do? Stages Moriarty’s resurrection. Brings back Sherlock, and, if Mary was in cahoots with him, smokes her out (she does sound suspiciously tense upon being told that Moriarty is still alive). Kills two birds with one stone. Yes, he reacts with surprise to the news, but he does so over the phone. He could very well be acting. He responds very calmly, after all.
I think Sherlock was counting on Mycroft. This dialogue is very suggestive:
JOHN: “The game is over.”
SHERLOCK: “The game is never over, John. But there may be some new players now. That’s okay. The east wind takes us all in the end.”
JOHN: “What was that?”
SHERLOCK: “It’s a story my brother told me when we were kids. The east wind, this terrifying force that lays waste to all in its path. Seeks out the unworthy and plucks them from the earth.”
Are you expecting the east wind to pluck Mary from the earth, Sherlock?
Then, when Mycroft calls Sherlock and asks how his exile is going, he replies “I’ve only been gone four minutes.”
We’ve seen him pass comment on Mycroft’s timing before - in the Baskerville labs in The Hounds of Baskerville and in Mycroft’s office in The Empty Hearse. Was he expecting to return? Quite possibly. So soon? Possibly not.
Perhaps Mycroft’s not slipping as much as Sherlock thinks he is.

wsswatson:

Another three episodes. Another series finished. Another set of surprises. Another cliffhanger.

As is to be expected, fans have been going wild, theories have been spreading like wildfire, and conversation is roaring.

I have a few theories of my own, and after a few rewatches, I’m ready to lay them all out. I’m going to try to lay them out chronologically so that you can consider them as and when you rewatch the episode, but some jumping about will be necessary.

So, here we go:

THESES: The woman we know as Mary Morstan was in cahoots with Moriarty. Sherlock was lying about trusting her. Mycroft saved Sherlock’s life.

Mary first.

Let’s have a think about the scene in which Mary shoots Sherlock. The first thing that leaped out at me was her clothing. Mary is dressed in the clothing of an assassin. People have been arguing that Mary has changed and left that life behind her. Has she really? She kept the clothes, and the gun. She kept them hidden from John, too. Even if she’s no longer ‘in business’, she hasn’t retired, either.

Now, let’s take a look at the shooting itself. Just before it takes place, the following dialogue occurs:

SHERLOCK: “Mary, whatever he’s got on you, let me help.”

MARY: “Oh, Sherlock, if you take one more step, I swear I will kill you.”

SHERLOCK: “No, Mrs Watson.* You won’t.”

*An appeal to Mary’s sentiment by referencing their shared connection to John?

Then, of course, she shoots him, and notice the look of surprise on Sherlock’s face:

His last word before he falls unconscious is “Mary?”

He was not expecting that, which supports my theory that she really did shoot to kill (bear with me).

Sherlock, in an attempt to save himself, enters his mind palace, where one of the first things that the Molly of his imagination says is: “You’re almost certainly going to die, so we need to focus.”

Then we have Mycroft: “It’s all very well having a mind palace, but you’ve only three seconds of consciousness left to use it.”

Then Mycroft says “What was directly behind you when you were murdered?”

Sherlock says “I haven’t been murdered yet!” to which Mycroft replies “Balance of probability, little brother.”

Now, remember that Molly and Mycroft are not really present - all of this takes place in Sherlock’s head. Conclusion? Sherlock thinks that Mary shot to kill.

She succeeded, too. His heart stopped. The surgeons moved away, they gave up. Sherlock died.

What saved him?

John arrived and spoke to him.

Then Moriarty, in Sherlock’s mind palace, said “…And John will cry buckets and buckets. It’s him I worry about the most. That wife! You’re letting him down, Sherlock. John Watson is definitely in danger.

Again, remember that Moriarty is not really the one speaking. This is all in Sherlock’s head. Sherlock fought his way back to life because he believed John to be in danger from Mary. Sherlock does not trust Mary, and he certainly doesn’t trust her with his best friend.

Then there’s what John said at the hospital: “His first word when he woke up? ‘Mary’!

He woke up thinking of her. He definitely does not trust her.

Look how she reacts to hearing that he’s alright, too:

That is not a look of relief.

Then Mary visits him, and says: “You don’t tell him. Sherlock! You don’t tell John. … Look at me, and tell me you’re not going to tell him.

If she was sorry, she would’ve said so. If she was sorry, there would have been at least a hint of remorse in her tone. There was not. Her tone was threatening. She didn’t ask him not to tell John, she told him, and by this point, we and Sherlock both know what she is capable of doing to people.

This is also proof of just how selfish Mary’s love for John is. When you love someone, really love them, your priority is their safety. Mary’s priority is not John’s safety - if she has such a dangerous past, the safest thing for John would be to come clean, because at some point, it’s possible that John might be targeted because of her (just as he has been because of Sherlock, and it was through Mary that Magnussen observed Sherlock’s reaction to John being placed in the fire).

It’s not “I’m sorry that I shot you. Even if I didn’t care about you one bit, I know that my husband does, and I am sorry to have caused him any pain through harming you.”

It’s “Don’t you dare tell my husband what I did, because then he will leave me.”

She loves John, certainly, but she is very, very selfish about it.

Of course, Sherlock’s still drowsy at that point. A little later, though, Janine visits, and just before she leaves, she says: “I’ll give your love to John and Mary.”

At this point, Sherlock’s face becomes determined, and he turns down the morphine tap. He gets ready to make his escape.

Cut to the mind palace, and look how Mary appears:

She’s dressed as she was the day she and Sherlock met. Which, by the way was suspicious in itself, as she appeared to have no idea who Sherlock was - “John? John, what is it? Oh, no, you’re- [Sherlock].” Sherlock was all over the papers. Everyone knew what he looked like, and someone so close to John certainly would. That implies to me that she knows more about him than she was willing to let on, and so pretended to know nothing at all. Liar.

Then look at how she reacts to discovering Sherlock’s ‘number 1 bolthole’:

That is a look of pure suspicion and trepidation. Not only does Sherlock not trust Mary, she doesn’t trust him either.

Now let’s talk about the dialogue back in 221b:

JOHN: “He knew who shot him. The bullet wound was here, so he was facing whoever it was.”

LESTRADE: “So why not tell us? Because he’s tracking them down himself-“

JOHN: “Or protecting them?”

LESTRADE: “Protecting the shooter - why?”

JOHN: “Protecting someone, then. But why would he care? He’s Sherlock. Who would he bother protecting?”

And this is the shot as he finishes speaking:

In this shot, if only very partially, is John, Lestrade and Mrs Hudson, the three people Sherlock risked his life to save when he jumped off the roof of Bart’s. If you want some subliminal messaging that Sherlock was not protecting the shooter, but, as John said, ‘someone’, there it is. At the center of the shot is John, who then, of course, comes to a realisation: he’s sitting in my armchair. He then asks:

"Mrs Hudson, why did Sherlock think I’d be moving back in here?"

The realisation hits him then. Sherlock was not protecting the shooter. He was protecting his best friend.

Let’s skip along a little bit. Mary goes to Leinster Gardens, where Sherlock calls her. He brings her to his bolthole. How does he describe that bolthole?

"The empty houses."

Let’s take a look at an extract from The Adventure of the Empty House:

I had imagined that we were bound for Baker Street, but Holmes stopped the cab at the corner of Cavendish Square. I observed that as he stepped out he gave a most searching glance to right and left, and at every subsequent street corner he took the utmost pains to assure that he was not followed. Our route was certainly a singular one. Holmes’s knowledge of the byways of London was extraordinary, and on this occasion he passed rapidly and with an assured step through a network of mews and stables, the very existence of which I had never known. We emerged at last into a small road, lined with old, gloomy houses, which led us into Manchester Street, and so to Blandford Street. Here he turned swiftly down a narrow passage, passed through a wooden gate into a deserted yard, and then opened with a key the back door of a house. We entered together, and he closed it behind us.

The place was pitch dark, but it was evident to me that it was an empty house. Our feet creaked and crackled over the bare planking, and my outstretched hand touched a wall from which the paper was hanging in ribbons. Holmes’s cold, thin fingers closed round my wrist and led me forward down a long hall, until I dimly saw the murky fanlight over the door. Here Holmes turned suddenly to the right, and we found ourselves in a large, square, empty room, heavily shadowed in the corners, but faintly lit in the centre from the lights of the street beyond. There was no lamp near, and the window was thick with dust, so that we could only just discern each other’s figures within. My companion put his hand upon my shoulder and his lips close to my ear.

“Do you know where we are?” he whispered.

“Surely that is Baker Street,” I answered, staring through the dim window.

“Exactly. We are in Camden House, which stands opposite to our own old quarters.”

“But why are we here?”

“Because it commands so excellent a view of that picturesque pile. Might I trouble you, my dear Watson, to draw a little nearer to the window, taking every precaution not to show yourself, and then to look up at our old rooms–the starting-point of so many of your little fairy-tales? We will see if my three years of absence have entirely taken away my power to surprise you.”

I crept forward and looked across at the familiar window. As my eyes fell upon it, I gave a gasp and a cry of amazement. The blind was down, and a strong light was burning in the room. The shadow of a man who was seated in a chair within was thrown in hard, black outline upon the luminous screen of the window. There was no mistaking the poise of the head, the squareness of the shoulders, the sharpness of the features. The face was turned half-round, and the effect was that of one of those black silhouettes which our grandparents loved to frame. It was a perfect reproduction of Holmes. So amazed was I that I threw out my hand to make sure that the man himself was standing beside me. He was quivering with silent laughter.

“Well?” said he.

“Good heavens!” I cried. “It is marvellous.”

“I trust that age doth not wither nor custom stale my infinite variety,” said he, and I recognized in his voice the joy and pride which the artist takes in his own creation. “It really is rather like me, is it not?”

“I should be prepared to swear that it was you.”

“The credit of the execution is due to Monsieur Oscar Meunier, of Grenoble, who spent some days in doing the moulding. It is a bust in wax. The rest I arranged myself during my visit to Baker Street this afternoon.”

“But why?”

“Because, my dear Watson, I had the strongest possible reason for wishing certain people to think that I was there when I was really elsewhere.”

“And you thought the rooms were watched?”

“I knew that they were watched.”

“By whom?”

“By my old enemies, Watson. By the charming society whose leader lies in the Reichenbach Fall. You must remember that they knew, and only they knew, that I was still alive. Sooner or later they believed that I should come back to my rooms. They watched them continuously, and this morning they saw me arrive.”

The specific enemy in question, who Holmes and Watson apprehend, is Colonel Sebastian Moran, the late Moriarty’s right-hand man, described thus:

Moran, Sebastian, Colonel. Unemployed. Formerly 1st Bangalore Pioneers. Born London, 1840. Son of Sir Augustus Moran, C. B., once British Minister to Persia. Educated Eton and Oxford. Served in Jowaki Campaign, Afghan Campaign, Charasiab (despatches), Sherpur, and Cabul. Author of Heavy Game of the Western Himalayas (1881); Three Months in the Jungle (1884). Address: Conduit Street. Clubs: The Anglo-Indian, the Tankerville, the Bagatelle Card Club.

On the margin was written, in Holmes’s precise hand:

The second most dangerous man in London.

A trained assassin, currently unemployed, who Holmes and Watson confront in an empty house. Remind you of anyone?

Let’s add to that her very suspicious behaviour regarding apparently not recognising Sherlock on the day they met. May she, like Moran, have known that Sherlock was alive, and have been watching him?

Here, again, Sherlock demonstrates that he does not trust Mary: “Remind you of anyone, Mary? A façade?”

His later demonstration of apparent trust is most certainly an act.

Almost as soon as Mary enters the building, her hand goes to her gun:

She certainly doesn’t have any qualms with killing Sherlock. She confirms this herself not long afterwards:

MARY: “You were very slow.”

SHERLOCK: “How good a shot are you?”

MARY: “How badly d’you wanna find out?”

Now, of course she doesn’t then actually kill him - that would ruin the narrative; the shooting of the coin has to serve as a suitable alternative. She of course shoots it excellently. Now, here comes the odd bit:

SHERLOCK: “And yet over a distance of six feet you failed to make a kill shot. That wasn’t a miss. It was surgery. I’ll take the case.”

And yet, it wasn’t a miss. It was a very good shot. Sherlock died. So why say it? I’ll come back to that.

MARY: “What case?”

SHERLOCK: “Yours. Why didn’t you come to me in the first place?”

MARY: “Because John can’t ever know that I lied to him. It would break him and I would lose him forever, and Sherlock, I will never let that happen. Please, understand, there is nothing in this world I would not do to stop that happening.”

Like killing one of the most intelligent and observant men in the world who also happens to be his best friend, for instance? Your selfishness is showing again there, Mary.

Now let’s take a look at the confrontation between Sherlock, John and Mary back in 221b:

JOHN: “You… What have I ever done? Hm? My whole life… to deserve you.”

SHERLOCK: “Everything.”

JOHN: “Sherlock, I’ve told you… Shut up.”

SHERLOCK: “No, I mean it, seriously, everything. Everything you’ve ever done is what you did.”

JOHN: “Sherlock, one more word and you will not need morphine.”

SHERLOCK: “You’re a doctor who went to war; you’re a man who couldn’t stay in the suburbs for more than a month without storming a crack den, beating up a junkie. Your best friend is a sociopath who solves crimes as an alternative to getting high. That’s me by the way - hello! Even the landlady used to run a drug cartel. […] John, you are addicted to a certain lifestyle. You’re abnormally attracted to dangerous situations and people. So is it truly such a surprise that the woman you fall in love with conforms to that pattern?”

JOHN: “But she wasn’t supposed to be like that! Why is she like that?”

SHERLOCK: “Because you chose her.”

At first, this seems cruel. It seems as though Sherlock is forcing the blame of the situation on John, and certainly, that’s how John takes it - “Why is everything… always… MY FAULT?”

However, might this not be more evidence for the Mary-as-Moriarty’s-ex-right-hand-(wo)man theory? She’s not dangerous because John chose her or vice versa, but she put herself in John’s path because he’s caught up in that dangerous lifestyle, and with Sherlock.

She is, after all, a nurse, and does that suit her? Presumably she’s taken innocent lives. If she had only taken the lives of bad people, why would John care? He’s done exactly the same, as she presumably knows - he was, after all, in the army in a protective role. Mary is not an altruist. She does not have a personality suited to nursing. She presumably trained as a nurse during her five years since taking Mary Morstan’s identity, too, and not an NHS nurse, either - she works privately at John’s clinic. Less background checks, then. It seems to me that Mary intentionally put herself in John’s path. The Moriarty connection is looking likelier and likelier.

Let’s go a bit further.

SHERLOCK: “John, listen, be calm and answer me. What is she?”

JOHN: “My lying wife.”

SHERLOCK: “No, what is she?”

JOHN: “And the woman who is carrying my child who has lied to me since the day I met her.”

SHERLOCK: “No. Not in this flat, not in this room, right here, right now, what is she?”

JOHN: “Okay. Your way. Always your way. Sit.”

MARY: “Why?”

JOHN: “Because that’s where they sit! The people who come in here with their stories. The clients - that’s all you are now, Mary. You’re a client. This is where you sit and talk and this is where we sit and listen. Then we decide if we want you or not.”

In this scene, John completely places his trust in Sherlock and disowns Mary. He also mentions that she is carrying his child. Let’s continue.

Mary hands John a memory stick:

SHERLOCK: “A.G.R.A. What’s that?”

MARY: “My initials. Everything about who I was is on there.”

Oh, really? You said you would do anything to prevent John from finding out the truth about you, and yet you just happened to be carrying all of the information about your past with you?

Liar.

For those of you who aren’t away, the initials are a reference to a Great Agra Treasure of The Sign of Four, which turns out to be missing, the case empty:

“That is all over,” I answered. “It was nothing. I will tell you no more gloomy details. Let us turn to something brighter. There is the treasure. What could be brighter than that? I got leave to bring it with me, thinking that it would interest you to be the first to see it.”

“It would be of the greatest interest to me,” she said. There was no eagerness in her voice, however. It had struck her, doubtless, that it might seem ungracious upon her part to be indifferent to a prize which had cost so much to win.

“What a pretty box!” she said, stooping over it. “This is Indian work, I suppose?”

“Yes; it is Benares metal-work.”

“And so heavy!” she exclaimed, trying to raise it. “The box alone must be of some value. Where is the key?”

“Small threw it into the Thames,” I answered. “I must borrow Mrs. Forrester’s poker.”

There was in the front a thick and broad hasp, wrought in the image of a sitting Buddha. Under this I thrust the end of the poker and twisted it outward as a lever. The hasp sprang open with a loud snap. With trembling fingers I flung back the lid. We both stood gazing in astonishment. The box was empty!

No wonder that it was heavy. The ironwork was two-thirds of an inch thick all round. It was massive, well made, and solid, like a chest constructed to carry things of great price, but not one shred or crumb of metal or jewellery lay within it. It was absolutely and completely empty.

“The treasure is lost,” said Miss Morstan calmly.

I don’t think that that memory stick contained the truth, the whole truth and nothing but the truth, do you?

Then let’s look at this speech of Sherlock’s:

"By your skill set, you are or were an intelligence agent. Your accent is currently English but I suspect you are not. You’re on the run from something. You’ve used your skills to disappear, Magnussen knows your secret, which is why you were going to kill him, and I assume you befriended Janine in order to get close to him.”

'Are' is not looking likely. Look what MI6 has to say about that role:

'What about secrecy? Well obviously the details of your work will be secret and we ask you not to discuss your application with anybody. That said, once you join us you'll be able to disclose your role to one or two close friends or family. We'll help you create a credible cover story for everyone else.'

So why haven’t you disclosed your role to John, Mary? Where’s your credible cover story? No, she’s not an intelligence officer anymore.

She has disclosed her role to someone, though. Remember how quickly she said “Oh, he would have needed a confidante!” in reference to Sherlock going on the run? You’re on the run too, Mary. Who’s your confidante?

Then there’s this:

MARY: “The stuff Magnussen has on me - I would go to prison for the rest of my life.

JOHN: “So you were just gonna kill him?”

MARY: “People like Magnussen should be killed, that’s why there are people like me.”

JOHN: “Perfect. So that’s what you were? An assassin? How could I not see that?”

MARY: “You did see that. And you married me. Because he’s right. It’s what you like.

She’d go to prison for the rest of her life? Not if she was still with the secret service. She worked for much nastier people than that.

Here we also see another nasty trait of Mary’s come to light: she’s emotionally abusive. She turns the blame of the situation away from herself and onto John. She did say she’d do anything to prevent him from leaving her.

Look at John’s face, how he responds:

He is devastated, furious, he certainly doesn’t look like he plans to forgive her. So why do we see him do exactly that?

Well, for one thing, she’s carrying his child. He evidently cares about that - when she falls unconscious, he says to Sherlock: “Did you just drug my pregnant wife?” Emphasis on the ‘pregnant’.

For another, Sherlock tells him to: “John, John! Magnussen is all that matters now. You can trust Mary. She saved my life.”

Prior to that, he claimed that she fired “One precise shot to incapacitate [him] in the hope that it would give [her] time to negotiate [his] silence.” Yet again, she quite literally killed him. There is no proof that she really did call an ambulance, either - the scene in which we see her doing so is a reconstruction of Sherlock’s claim, and I used to have a horse. I saw lots of accidents. Multiple people would call an ambulance, and upon doing so, later people to call would be told that an ambulance had already been sent out to that particular incident. That didn’t happen to John. Perhaps there was good traffic that day, or an ambulance happened to be in the area. Besides, Sherlock fell unconscious within three seconds, went into shock (which can cause memory loss) and was dosed with morphine (which causes disorientation). Hardly the right circumstances to provide for a thorough analysis of the situation.

So why does Sherlock insist that Mary is trustworthy when he quite obviously doesn’t trust her? My guess is that he wants to placate her. He does, after all, say this in her presence. He wants to lull her into a sense of false security. We know that he wants what Magnussen has on her - “I want everything you’ve got on Mary”; “In return for the password, you will give me any material in your possession pertaining to the woman I know as Mary Watson” - but we don’t know why. Is it really to protect her? Or is it because he wants to know her secret?

John may be in on that - after all, he and Mary did undergo “months of silence”, and the timing of their ‘reconciliation’, just before the drugs took effect and everyone fell unconscious, was fortunate. I’m sure Sherlock invited John AND Mary to Christmas dinner for a reason. Perhaps John is just burdened by guilt and a sense of duty, and really is trying to forgive her, but the evidence suggests that he’s highly suspicious of her, too.

There’s also the fact that, when reconciling with her, he says “I’ve thought long and hard about what I want to say to you. These are prepared words, Mary. Chosen these words with care.” He also later says “I am very pissed off and it will come out now and then.”

John is not a good liar. Sherlock established this in The Empty Hearse:

JOHN: “One word, Sherlock, that is all I would’ve needed! One word to let me know that you were alive!”

SHERLOCK: “I’ve nearly been in contact so many times but I worried that, you know, you might say something indiscreet… You know, let the cat out of the bag.”

Now, nobody sounds natural when they speak from rehearsal. John’s repeated claim that that is what he’s doing, as well as letting Mary know that he will lose his temper with her in the future, is the perfect cover for an act by a not particularly good actor.

The editing of this section is important, too. It cuts between the confrontation scene in 221b and the reconciliation scene. That, to me, suggests that we are not supposed to buy into John’s forgiveness. It’s hard to, when we’ve just seen him so devastated and fuming.

So, onto the Magnussen scene. He really solidifies my theory that she was in cahoots with Moriarty. Let’s look at some of the things he says about her:

"I’m not a murderer, unlike your wife.”

'Murderer' is an interesting choice of word. It suggests worse than working with the secret service. If that was all he meant, presumably he would've said 'killer'. There are implications behind the word 'murderer' - implications of immorality.

"Oh, she’s bad, that one. So many dead people. You should see what I’ve seen."

Again, suggestions of immorality.

And my favourite:

"All those wet jobs for the CIA. Ooh! She’s gone a bit freelance now, bad girl. [laughter] Oh, she’s so wicked. I can really see why you like her.”

She clearly worked for someone who was not at all moral. Again, my bets are on Moriarty.

So why did Sherlock shoot Magnussen?

Well, let’s take a look at his expression upon discovering that Magnussen apparently keeps all of his blackmail material in his mind:

He looks horrified. Why? Because he cannot obtain the information and hence protect Mary? Or because he cannot obtain the information and hence learn her secret and hence protect John?

Then let’s consider what Magnussen says to John shortly before Sherlock shoots him:

"I know who Mary hurt and killed. I know where to find people who hate her. I know where they live. I know their phone numbers. All in my mind palace. I could phone them right now and tear your whole life down. And I will. Unless you let me flick your face."

After that, killing Magnussen seems to be Sherlock’s safest bet at protecting John. Mary may well be a risk to him, but so are all the people who hate her. John would be be fighting a war on two fronts if Magnussen set Mary’s enemies on her.

Then there’s the fact that Mycroft’s present (and in control). I think Sherlock suspects that Mycroft would protect him, and therefore allow him to continue to protect John. After all, as he said at the cottage: “Your loss would break my heart.” Indeed, he immediately commands: “Do not fire! Do not fire on Sherlock Holmes! Do not fire!”

In fact, I believe that Mycroft is the hero of this story.

Earlier on, at the cottage, he said to Sherlock:

"I have, by the way, a job offer I should like you to decline. […] MI6. They want to place you back into Eastern Europe. An undercover assignment that will prove fatal to you in, I think, about six months."

This is, of course, the assignment that Mycroft arranges for Sherlock to be sent on rather than being sent to prison for killing Magnussen. Now, would Mycroft do that without a plan? Would he really rather send Sherlock to his death than have him in prison? After all, “There will always come a time when we need Sherlock Holmes.”

Remember, too, how much Mycroft knows. He’s more intelligent than Sherlock, and Sherlock invited Mary to the family home when Mycroft was there. I suspect that Mycroft is well aware that something is up with Mary.

So, what does he do? Stages Moriarty’s resurrection. Brings back Sherlock, and, if Mary was in cahoots with him, smokes her out (she does sound suspiciously tense upon being told that Moriarty is still alive). Kills two birds with one stone. Yes, he reacts with surprise to the news, but he does so over the phone. He could very well be acting. He responds very calmly, after all.

I think Sherlock was counting on Mycroft. This dialogue is very suggestive:

JOHN: “The game is over.”

SHERLOCK: “The game is never over, John. But there may be some new players now. That’s okay. The east wind takes us all in the end.

JOHN: “What was that?”

SHERLOCK: “It’s a story my brother told me when we were kids. The east wind, this terrifying force that lays waste to all in its path. Seeks out the unworthy and plucks them from the earth.

Are you expecting the east wind to pluck Mary from the earth, Sherlock?

Then, when Mycroft calls Sherlock and asks how his exile is going, he replies “I’ve only been gone four minutes.”

We’ve seen him pass comment on Mycroft’s timing before - in the Baskerville labs in The Hounds of Baskerville and in Mycroft’s office in The Empty Hearse. Was he expecting to return? Quite possibly. So soon? Possibly not.

Perhaps Mycroft’s not slipping as much as Sherlock thinks he is.

chilledchaosofficial
wsswatson:

Another three episodes. Another series finished. Another set of surprises. Another cliffhanger.
As is to be expected, fans have been going wild, theories have been spreading like wildfire, and conversation is roaring.
I have a few theories of my own, and after a few rewatches, I’m ready to lay them all out. I’m going to try to lay them out chronologically so that you can consider them as and when you rewatch the episode, but some jumping about will be necessary.
So, here we go:
THESES: The woman we know as Mary Morstan was in cahoots with Moriarty. Sherlock was lying about trusting her. Mycroft saved Sherlock’s life.
Mary first.
Let’s have a think about the scene in which Mary shoots Sherlock. The first thing that leaped out at me was her clothing. Mary is dressed in the clothing of an assassin. People have been arguing that Mary has changed and left that life behind her. Has she really? She kept the clothes, and the gun. She kept them hidden from John, too. Even if she’s no longer ‘in business’, she hasn’t retired, either.
Now, let’s take a look at the shooting itself. Just before it takes place, the following dialogue occurs:
SHERLOCK: “Mary, whatever he’s got on you, let me help.”
MARY: “Oh, Sherlock, if you take one more step, I swear I will kill you.”
SHERLOCK: “No, Mrs Watson.* You won’t.”
*An appeal to Mary’s sentiment by referencing their shared connection to John?
Then, of course, she shoots him, and notice the look of surprise on Sherlock’s face:

His last word before he falls unconscious is “Mary?”
He was not expecting that, which supports my theory that she really did shoot to kill (bear with me).
Sherlock, in an attempt to save himself, enters his mind palace, where one of the first things that the Molly of his imagination says is: “You’re almost certainly going to die, so we need to focus.”
Then we have Mycroft: “It’s all very well having a mind palace, but you’ve only three seconds of consciousness left to use it.”
Then Mycroft says “What was directly behind you when you were murdered?”
Sherlock says “I haven’t been murdered yet!” to which Mycroft replies “Balance of probability, little brother.”
Now, remember that Molly and Mycroft are not really present - all of this takes place in Sherlock’s head. Conclusion? Sherlock thinks that Mary shot to kill.
She succeeded, too. His heart stopped. The surgeons moved away, they gave up. Sherlock died.
What saved him?
John arrived and spoke to him.
Then Moriarty, in Sherlock’s mind palace, said “…And John will cry buckets and buckets. It’s him I worry about the most. That wife! You’re letting him down, Sherlock. John Watson is definitely in danger.”
Again, remember that Moriarty is not really the one speaking. This is all in Sherlock’s head. Sherlock fought his way back to life because he believed John to be in danger from Mary. Sherlock does not trust Mary, and he certainly doesn’t trust her with his best friend.
Then there’s what John said at the hospital: “His first word when he woke up? ‘Mary’!”
He woke up thinking of her. He definitely does not trust her.
Look how she reacts to hearing that he’s alright, too:

That is not a look of relief.
Then Mary visits him, and says: “You don’t tell him. Sherlock! You don’t tell John. … Look at me, and tell me you’re not going to tell him.”
If she was sorry, she would’ve said so. If she was sorry, there would have been at least a hint of remorse in her tone. There was not. Her tone was threatening. She didn’t ask him not to tell John, she told him, and by this point, we and Sherlock both know what she is capable of doing to people.
This is also proof of just how selfish Mary’s love for John is. When you love someone, really love them, your priority is their safety. Mary’s priority is not John’s safety - if she has such a dangerous past, the safest thing for John would be to come clean, because at some point, it’s possible that John might be targeted because of her (just as he has been because of Sherlock, and it was through Mary that Magnussen observed Sherlock’s reaction to John being placed in the fire).
It’s not “I’m sorry that I shot you. Even if I didn’t care about you one bit, I know that my husband does, and I am sorry to have caused him any pain through harming you.”
It’s “Don’t you dare tell my husband what I did, because then he will leave me.”
She loves John, certainly, but she is very, very selfish about it.
Of course, Sherlock’s still drowsy at that point. A little later, though, Janine visits, and just before she leaves, she says: “I’ll give your love to John and Mary.”
At this point, Sherlock’s face becomes determined, and he turns down the morphine tap. He gets ready to make his escape.
Cut to the mind palace, and look how Mary appears:

She’s dressed as she was the day she and Sherlock met. Which, by the way was suspicious in itself, as she appeared to have no idea who Sherlock was - “John? John, what is it? Oh, no, you’re- [Sherlock].” Sherlock was all over the papers. Everyone knew what he looked like, and someone so close to John certainly would. That implies to me that she knows more about him than she was willing to let on, and so pretended to know nothing at all. Liar.
Then look at how she reacts to discovering Sherlock’s ‘number 1 bolthole’:


That is a look of pure suspicion and trepidation. Not only does Sherlock not trust Mary, she doesn’t trust him either.
Now let’s talk about the dialogue back in 221b:
JOHN: “He knew who shot him. The bullet wound was here, so he was facing whoever it was.”
LESTRADE: “So why not tell us? Because he’s tracking them down himself-“
JOHN: “Or protecting them?”
LESTRADE: “Protecting the shooter - why?”
JOHN: “Protecting someone, then. But why would he care? He’s Sherlock. Who would he bother protecting?”
And this is the shot as he finishes speaking:

In this shot, if only very partially, is John, Lestrade and Mrs Hudson, the three people Sherlock risked his life to save when he jumped off the roof of Bart’s. If you want some subliminal messaging that Sherlock was not protecting the shooter, but, as John said, ‘someone’, there it is. At the center of the shot is John, who then, of course, comes to a realisation: he’s sitting in my armchair. He then asks:
"Mrs Hudson, why did Sherlock think I’d be moving back in here?"
The realisation hits him then. Sherlock was not protecting the shooter. He was protecting his best friend.
Let’s skip along a little bit. Mary goes to Leinster Gardens, where Sherlock calls her. He brings her to his bolthole. How does he describe that bolthole?
"The empty houses."
Let’s take a look at an extract from The Adventure of the Empty House:

I had imagined that we were bound for Baker Street, but Holmes stopped the cab at the corner of Cavendish Square. I observed that as he stepped out he gave a most searching glance to right and left, and at every subsequent street corner he took the utmost pains to assure that he was not followed. Our route was certainly a singular one. Holmes’s knowledge of the byways of London was extraordinary, and on this occasion he passed rapidly and with an assured step through a network of mews and stables, the very existence of which I had never known. We emerged at last into a small road, lined with old, gloomy houses, which led us into Manchester Street, and so to Blandford Street. Here he turned swiftly down a narrow passage, passed through a wooden gate into a deserted yard, and then opened with a key the back door of a house. We entered together, and he closed it behind us.
The place was pitch dark, but it was evident to me that it was an empty house. Our feet creaked and crackled over the bare planking, and my outstretched hand touched a wall from which the paper was hanging in ribbons. Holmes’s cold, thin fingers closed round my wrist and led me forward down a long hall, until I dimly saw the murky fanlight over the door. Here Holmes turned suddenly to the right, and we found ourselves in a large, square, empty room, heavily shadowed in the corners, but faintly lit in the centre from the lights of the street beyond. There was no lamp near, and the window was thick with dust, so that we could only just discern each other’s figures within. My companion put his hand upon my shoulder and his lips close to my ear.
“Do you know where we are?” he whispered.
“Surely that is Baker Street,” I answered, staring through the dim window.
“Exactly. We are in Camden House, which stands opposite to our own old quarters.”
“But why are we here?”
“Because it commands so excellent a view of that picturesque pile. Might I trouble you, my dear Watson, to draw a little nearer to the window, taking every precaution not to show yourself, and then to look up at our old rooms–the starting-point of so many of your little fairy-tales? We will see if my three years of absence have entirely taken away my power to surprise you.”
I crept forward and looked across at the familiar window. As my eyes fell upon it, I gave a gasp and a cry of amazement. The blind was down, and a strong light was burning in the room. The shadow of a man who was seated in a chair within was thrown in hard, black outline upon the luminous screen of the window. There was no mistaking the poise of the head, the squareness of the shoulders, the sharpness of the features. The face was turned half-round, and the effect was that of one of those black silhouettes which our grandparents loved to frame. It was a perfect reproduction of Holmes. So amazed was I that I threw out my hand to make sure that the man himself was standing beside me. He was quivering with silent laughter.
“Well?” said he.
“Good heavens!” I cried. “It is marvellous.”
“I trust that age doth not wither nor custom stale my infinite variety,” said he, and I recognized in his voice the joy and pride which the artist takes in his own creation. “It really is rather like me, is it not?”
“I should be prepared to swear that it was you.”
“The credit of the execution is due to Monsieur Oscar Meunier, of Grenoble, who spent some days in doing the moulding. It is a bust in wax. The rest I arranged myself during my visit to Baker Street this afternoon.”
“But why?”
“Because, my dear Watson, I had the strongest possible reason for wishing certain people to think that I was there when I was really elsewhere.”
“And you thought the rooms were watched?”
“I knew that they were watched.”
“By whom?”
“By my old enemies, Watson. By the charming society whose leader lies in the Reichenbach Fall. You must remember that they knew, and only they knew, that I was still alive. Sooner or later they believed that I should come back to my rooms. They watched them continuously, and this morning they saw me arrive.”

The specific enemy in question, who Holmes and Watson apprehend, is Colonel Sebastian Moran, the late Moriarty’s right-hand man, described thus:

Moran, Sebastian, Colonel. Unemployed. Formerly 1st Bangalore Pioneers. Born London, 1840. Son of Sir Augustus Moran, C. B., once British Minister to Persia. Educated Eton and Oxford. Served in Jowaki Campaign, Afghan Campaign, Charasiab (despatches), Sherpur, and Cabul. Author of Heavy Game of the Western Himalayas (1881); Three Months in the Jungle (1884). Address: Conduit Street. Clubs: The Anglo-Indian, the Tankerville, the Bagatelle Card Club.
On the margin was written, in Holmes’s precise hand:
The second most dangerous man in London.

A trained assassin, currently unemployed, who Holmes and Watson confront in an empty house. Remind you of anyone?
Let’s add to that her very suspicious behaviour regarding apparently not recognising Sherlock on the day they met. May she, like Moran, have known that Sherlock was alive, and have been watching him?
Here, again, Sherlock demonstrates that he does not trust Mary: “Remind you of anyone, Mary? A façade?”
His later demonstration of apparent trust is most certainly an act.
Almost as soon as Mary enters the building, her hand goes to her gun:

She certainly doesn’t have any qualms with killing Sherlock. She confirms this herself not long afterwards:
MARY: “You were very slow.”
SHERLOCK: “How good a shot are you?”
MARY: “How badly d’you wanna find out?”
Now, of course she doesn’t then actually kill him - that would ruin the narrative; the shooting of the coin has to serve as a suitable alternative. She of course shoots it excellently. Now, here comes the odd bit:
SHERLOCK: “And yet over a distance of six feet you failed to make a kill shot. That wasn’t a miss. It was surgery. I’ll take the case.”
And yet, it wasn’t a miss. It was a very good shot. Sherlock died. So why say it? I’ll come back to that.
MARY: “What case?”
SHERLOCK: “Yours. Why didn’t you come to me in the first place?”
MARY: “Because John can’t ever know that I lied to him. It would break him and I would lose him forever, and Sherlock, I will never let that happen. Please, understand, there is nothing in this world I would not do to stop that happening.”
Like killing one of the most intelligent and observant men in the world who also happens to be his best friend, for instance? Your selfishness is showing again there, Mary.
Now let’s take a look at the confrontation between Sherlock, John and Mary back in 221b:
JOHN: “You… What have I ever done? Hm? My whole life… to deserve you.”
SHERLOCK: “Everything.”
JOHN: “Sherlock, I’ve told you… Shut up.”
SHERLOCK: “No, I mean it, seriously, everything. Everything you’ve ever done is what you did.”
JOHN: “Sherlock, one more word and you will not need morphine.”
SHERLOCK: “You’re a doctor who went to war; you’re a man who couldn’t stay in the suburbs for more than a month without storming a crack den, beating up a junkie. Your best friend is a sociopath who solves crimes as an alternative to getting high. That’s me by the way - hello! Even the landlady used to run a drug cartel. […] John, you are addicted to a certain lifestyle. You’re abnormally attracted to dangerous situations and people. So is it truly such a surprise that the woman you fall in love with conforms to that pattern?”
JOHN: “But she wasn’t supposed to be like that! Why is she like that?”
SHERLOCK: “Because you chose her.”
At first, this seems cruel. It seems as though Sherlock is forcing the blame of the situation on John, and certainly, that’s how John takes it - “Why is everything… always… MY FAULT?”
However, might this not be more evidence for the Mary-as-Moriarty’s-ex-right-hand-(wo)man theory? She’s not dangerous because John chose her or vice versa, but she put herself in John’s path because he’s caught up in that dangerous lifestyle, and with Sherlock.
She is, after all, a nurse, and does that suit her? Presumably she’s taken innocent lives. If she had only taken the lives of bad people, why would John care? He’s done exactly the same, as she presumably knows - he was, after all, in the army in a protective role. Mary is not an altruist. She does not have a personality suited to nursing. She presumably trained as a nurse during her five years since taking Mary Morstan’s identity, too, and not an NHS nurse, either - she works privately at John’s clinic. Less background checks, then. It seems to me that Mary intentionally put herself in John’s path. The Moriarty connection is looking likelier and likelier.
Let’s go a bit further.
SHERLOCK: “John, listen, be calm and answer me. What is she?”
JOHN: “My lying wife.”
SHERLOCK: “No, what is she?”
JOHN: “And the woman who is carrying my child who has lied to me since the day I met her.”
SHERLOCK: “No. Not in this flat, not in this room, right here, right now, what is she?”
JOHN: “Okay. Your way. Always your way. Sit.”
MARY: “Why?”
JOHN: “Because that’s where they sit! The people who come in here with their stories. The clients - that’s all you are now, Mary. You’re a client. This is where you sit and talk and this is where we sit and listen. Then we decide if we want you or not.”
In this scene, John completely places his trust in Sherlock and disowns Mary. He also mentions that she is carrying his child. Let’s continue.
Mary hands John a memory stick:

SHERLOCK: “A.G.R.A. What’s that?”
MARY: “My initials. Everything about who I was is on there.”
Oh, really? You said you would do anything to prevent John from finding out the truth about you, and yet you just happened to be carrying all of the information about your past with you?
Liar.
For those of you who aren’t away, the initials are a reference to a Great Agra Treasure of The Sign of Four, which turns out to be missing, the case empty:

“That is all over,” I answered. “It was nothing. I will tell you no more gloomy details. Let us turn to something brighter. There is the treasure. What could be brighter than that? I got leave to bring it with me, thinking that it would interest you to be the first to see it.”
“It would be of the greatest interest to me,” she said. There was no eagerness in her voice, however. It had struck her, doubtless, that it might seem ungracious upon her part to be indifferent to a prize which had cost so much to win.
“What a pretty box!” she said, stooping over it. “This is Indian work, I suppose?”
“Yes; it is Benares metal-work.”
“And so heavy!” she exclaimed, trying to raise it. “The box alone must be of some value. Where is the key?”
“Small threw it into the Thames,” I answered. “I must borrow Mrs. Forrester’s poker.”
There was in the front a thick and broad hasp, wrought in the image of a sitting Buddha. Under this I thrust the end of the poker and twisted it outward as a lever. The hasp sprang open with a loud snap. With trembling fingers I flung back the lid. We both stood gazing in astonishment. The box was empty!
No wonder that it was heavy. The ironwork was two-thirds of an inch thick all round. It was massive, well made, and solid, like a chest constructed to carry things of great price, but not one shred or crumb of metal or jewellery lay within it. It was absolutely and completely empty.
“The treasure is lost,” said Miss Morstan calmly.

I don’t think that that memory stick contained the truth, the whole truth and nothing but the truth, do you?
Then let’s look at this speech of Sherlock’s:
"By your skill set, you are or were an intelligence agent. Your accent is currently English but I suspect you are not. You’re on the run from something. You’ve used your skills to disappear, Magnussen knows your secret, which is why you were going to kill him, and I assume you befriended Janine in order to get close to him.”
'Are' is not looking likely. Look what MI6 has to say about that role:
'What about secrecy? Well obviously the details of your work will be secret and we ask you not to discuss your application with anybody. That said, once you join us you'll be able to disclose your role to one or two close friends or family. We'll help you create a credible cover story for everyone else.'
So why haven’t you disclosed your role to John, Mary? Where’s your credible cover story? No, she’s not an intelligence officer anymore.
She has disclosed her role to someone, though. Remember how quickly she said “Oh, he would have needed a confidante!” in reference to Sherlock going on the run? You’re on the run too, Mary. Who’s your confidante?
Then there’s this:
MARY: “The stuff Magnussen has on me - I would go to prison for the rest of my life.”
JOHN: “So you were just gonna kill him?”
MARY: “People like Magnussen should be killed, that’s why there are people like me.”
JOHN: “Perfect. So that’s what you were? An assassin? How could I not see that?”
MARY: “You did see that. And you married me. Because he’s right. It’s what you like.”
She’d go to prison for the rest of her life? Not if she was still with the secret service. She worked for much nastier people than that.
Here we also see another nasty trait of Mary’s come to light: she’s emotionally abusive. She turns the blame of the situation away from herself and onto John. She did say she’d do anything to prevent him from leaving her.
Look at John’s face, how he responds:

He is devastated, furious, he certainly doesn’t look like he plans to forgive her. So why do we see him do exactly that?
Well, for one thing, she’s carrying his child. He evidently cares about that - when she falls unconscious, he says to Sherlock: “Did you just drug my pregnant wife?” Emphasis on the ‘pregnant’.
For another, Sherlock tells him to: “John, John! Magnussen is all that matters now. You can trust Mary. She saved my life.”
Prior to that, he claimed that she fired “One precise shot to incapacitate [him] in the hope that it would give [her] time to negotiate [his] silence.” Yet again, she quite literally killed him. There is no proof that she really did call an ambulance, either - the scene in which we see her doing so is a reconstruction of Sherlock’s claim, and I used to have a horse. I saw lots of accidents. Multiple people would call an ambulance, and upon doing so, later people to call would be told that an ambulance had already been sent out to that particular incident. That didn’t happen to John. Perhaps there was good traffic that day, or an ambulance happened to be in the area. Besides, Sherlock fell unconscious within three seconds, went into shock (which can cause memory loss) and was dosed with morphine (which causes disorientation). Hardly the right circumstances to provide for a thorough analysis of the situation.
So why does Sherlock insist that Mary is trustworthy when he quite obviously doesn’t trust her? My guess is that he wants to placate her. He does, after all, say this in her presence. He wants to lull her into a sense of false security. We know that he wants what Magnussen has on her - “I want everything you’ve got on Mary”; “In return for the password, you will give me any material in your possession pertaining to the woman I know as Mary Watson” - but we don’t know why. Is it really to protect her? Or is it because he wants to know her secret?
John may be in on that - after all, he and Mary did undergo “months of silence”, and the timing of their ‘reconciliation’, just before the drugs took effect and everyone fell unconscious, was fortunate. I’m sure Sherlock invited John AND Mary to Christmas dinner for a reason. Perhaps John is just burdened by guilt and a sense of duty, and really is trying to forgive her, but the evidence suggests that he’s highly suspicious of her, too.
There’s also the fact that, when reconciling with her, he says “I’ve thought long and hard about what I want to say to you. These are prepared words, Mary. Chosen these words with care.” He also later says “I am very pissed off and it will come out now and then.”
John is not a good liar. Sherlock established this in The Empty Hearse:
JOHN: “One word, Sherlock, that is all I would’ve needed! One word to let me know that you were alive!”
SHERLOCK: “I’ve nearly been in contact so many times but I worried that, you know, you might say something indiscreet… You know, let the cat out of the bag.”
Now, nobody sounds natural when they speak from rehearsal. John’s repeated claim that that is what he’s doing, as well as letting Mary know that he will lose his temper with her in the future, is the perfect cover for an act by a not particularly good actor.
The editing of this section is important, too. It cuts between the confrontation scene in 221b and the reconciliation scene. That, to me, suggests that we are not supposed to buy into John’s forgiveness. It’s hard to, when we’ve just seen him so devastated and fuming.
So, onto the Magnussen scene. He really solidifies my theory that she was in cahoots with Moriarty. Let’s look at some of the things he says about her:
"I’m not a murderer, unlike your wife.”
'Murderer' is an interesting choice of word. It suggests worse than working with the secret service. If that was all he meant, presumably he would've said 'killer'. There are implications behind the word 'murderer' - implications of immorality.
"Oh, she’s bad, that one. So many dead people. You should see what I’ve seen."
Again, suggestions of immorality.
And my favourite:
"All those wet jobs for the CIA. Ooh! She’s gone a bit freelance now, bad girl. [laughter] Oh, she’s so wicked. I can really see why you like her.”
She clearly worked for someone who was not at all moral. Again, my bets are on Moriarty.
So why did Sherlock shoot Magnussen?
Well, let’s take a look at his expression upon discovering that Magnussen apparently keeps all of his blackmail material in his mind:

He looks horrified. Why? Because he cannot obtain the information and hence protect Mary? Or because he cannot obtain the information and hence learn her secret and hence protect John?
Then let’s consider what Magnussen says to John shortly before Sherlock shoots him:
"I know who Mary hurt and killed. I know where to find people who hate her. I know where they live. I know their phone numbers. All in my mind palace. I could phone them right now and tear your whole life down. And I will. Unless you let me flick your face."
After that, killing Magnussen seems to be Sherlock’s safest bet at protecting John. Mary may well be a risk to him, but so are all the people who hate her. John would be be fighting a war on two fronts if Magnussen set Mary’s enemies on her.
Then there’s the fact that Mycroft’s present (and in control). I think Sherlock suspects that Mycroft would protect him, and therefore allow him to continue to protect John. After all, as he said at the cottage: “Your loss would break my heart.” Indeed, he immediately commands: “Do not fire! Do not fire on Sherlock Holmes! Do not fire!”
In fact, I believe that Mycroft is the hero of this story.
Earlier on, at the cottage, he said to Sherlock:
"I have, by the way, a job offer I should like you to decline. […] MI6. They want to place you back into Eastern Europe. An undercover assignment that will prove fatal to you in, I think, about six months."
This is, of course, the assignment that Mycroft arranges for Sherlock to be sent on rather than being sent to prison for killing Magnussen. Now, would Mycroft do that without a plan? Would he really rather send Sherlock to his death than have him in prison? After all, “There will always come a time when we need Sherlock Holmes.”
Remember, too, how much Mycroft knows. He’s more intelligent than Sherlock, and Sherlock invited Mary to the family home when Mycroft was there. I suspect that Mycroft is well aware that something is up with Mary.
So, what does he do? Stages Moriarty’s resurrection. Brings back Sherlock, and, if Mary was in cahoots with him, smokes her out (she does sound suspiciously tense upon being told that Moriarty is still alive). Kills two birds with one stone. Yes, he reacts with surprise to the news, but he does so over the phone. He could very well be acting. He responds very calmly, after all.
I think Sherlock was counting on Mycroft. This dialogue is very suggestive:
JOHN: “The game is over.”
SHERLOCK: “The game is never over, John. But there may be some new players now. That’s okay. The east wind takes us all in the end.”
JOHN: “What was that?”
SHERLOCK: “It’s a story my brother told me when we were kids. The east wind, this terrifying force that lays waste to all in its path. Seeks out the unworthy and plucks them from the earth.”
Are you expecting the east wind to pluck Mary from the earth, Sherlock?
Then, when Mycroft calls Sherlock and asks how his exile is going, he replies “I’ve only been gone four minutes.”
We’ve seen him pass comment on Mycroft’s timing before - in the Baskerville labs in The Hounds of Baskerville and in Mycroft’s office in The Empty Hearse. Was he expecting to return? Quite possibly. So soon? Possibly not.
Perhaps Mycroft’s not slipping as much as Sherlock thinks he is.

wsswatson:

Another three episodes. Another series finished. Another set of surprises. Another cliffhanger.

As is to be expected, fans have been going wild, theories have been spreading like wildfire, and conversation is roaring.

I have a few theories of my own, and after a few rewatches, I’m ready to lay them all out. I’m going to try to lay them out chronologically so that you can consider them as and when you rewatch the episode, but some jumping about will be necessary.

So, here we go:

THESES: The woman we know as Mary Morstan was in cahoots with Moriarty. Sherlock was lying about trusting her. Mycroft saved Sherlock’s life.

Mary first.

Let’s have a think about the scene in which Mary shoots Sherlock. The first thing that leaped out at me was her clothing. Mary is dressed in the clothing of an assassin. People have been arguing that Mary has changed and left that life behind her. Has she really? She kept the clothes, and the gun. She kept them hidden from John, too. Even if she’s no longer ‘in business’, she hasn’t retired, either.

Now, let’s take a look at the shooting itself. Just before it takes place, the following dialogue occurs:

SHERLOCK: “Mary, whatever he’s got on you, let me help.”

MARY: “Oh, Sherlock, if you take one more step, I swear I will kill you.”

SHERLOCK: “No, Mrs Watson.* You won’t.”

*An appeal to Mary’s sentiment by referencing their shared connection to John?

Then, of course, she shoots him, and notice the look of surprise on Sherlock’s face:

His last word before he falls unconscious is “Mary?”

He was not expecting that, which supports my theory that she really did shoot to kill (bear with me).

Sherlock, in an attempt to save himself, enters his mind palace, where one of the first things that the Molly of his imagination says is: “You’re almost certainly going to die, so we need to focus.”

Then we have Mycroft: “It’s all very well having a mind palace, but you’ve only three seconds of consciousness left to use it.”

Then Mycroft says “What was directly behind you when you were murdered?”

Sherlock says “I haven’t been murdered yet!” to which Mycroft replies “Balance of probability, little brother.”

Now, remember that Molly and Mycroft are not really present - all of this takes place in Sherlock’s head. Conclusion? Sherlock thinks that Mary shot to kill.

She succeeded, too. His heart stopped. The surgeons moved away, they gave up. Sherlock died.

What saved him?

John arrived and spoke to him.

Then Moriarty, in Sherlock’s mind palace, said “…And John will cry buckets and buckets. It’s him I worry about the most. That wife! You’re letting him down, Sherlock. John Watson is definitely in danger.

Again, remember that Moriarty is not really the one speaking. This is all in Sherlock’s head. Sherlock fought his way back to life because he believed John to be in danger from Mary. Sherlock does not trust Mary, and he certainly doesn’t trust her with his best friend.

Then there’s what John said at the hospital: “His first word when he woke up? ‘Mary’!

He woke up thinking of her. He definitely does not trust her.

Look how she reacts to hearing that he’s alright, too:

That is not a look of relief.

Then Mary visits him, and says: “You don’t tell him. Sherlock! You don’t tell John. … Look at me, and tell me you’re not going to tell him.

If she was sorry, she would’ve said so. If she was sorry, there would have been at least a hint of remorse in her tone. There was not. Her tone was threatening. She didn’t ask him not to tell John, she told him, and by this point, we and Sherlock both know what she is capable of doing to people.

This is also proof of just how selfish Mary’s love for John is. When you love someone, really love them, your priority is their safety. Mary’s priority is not John’s safety - if she has such a dangerous past, the safest thing for John would be to come clean, because at some point, it’s possible that John might be targeted because of her (just as he has been because of Sherlock, and it was through Mary that Magnussen observed Sherlock’s reaction to John being placed in the fire).

It’s not “I’m sorry that I shot you. Even if I didn’t care about you one bit, I know that my husband does, and I am sorry to have caused him any pain through harming you.”

It’s “Don’t you dare tell my husband what I did, because then he will leave me.”

She loves John, certainly, but she is very, very selfish about it.

Of course, Sherlock’s still drowsy at that point. A little later, though, Janine visits, and just before she leaves, she says: “I’ll give your love to John and Mary.”

At this point, Sherlock’s face becomes determined, and he turns down the morphine tap. He gets ready to make his escape.

Cut to the mind palace, and look how Mary appears:

She’s dressed as she was the day she and Sherlock met. Which, by the way was suspicious in itself, as she appeared to have no idea who Sherlock was - “John? John, what is it? Oh, no, you’re- [Sherlock].” Sherlock was all over the papers. Everyone knew what he looked like, and someone so close to John certainly would. That implies to me that she knows more about him than she was willing to let on, and so pretended to know nothing at all. Liar.

Then look at how she reacts to discovering Sherlock’s ‘number 1 bolthole’:

That is a look of pure suspicion and trepidation. Not only does Sherlock not trust Mary, she doesn’t trust him either.

Now let’s talk about the dialogue back in 221b:

JOHN: “He knew who shot him. The bullet wound was here, so he was facing whoever it was.”

LESTRADE: “So why not tell us? Because he’s tracking them down himself-“

JOHN: “Or protecting them?”

LESTRADE: “Protecting the shooter - why?”

JOHN: “Protecting someone, then. But why would he care? He’s Sherlock. Who would he bother protecting?”

And this is the shot as he finishes speaking:

In this shot, if only very partially, is John, Lestrade and Mrs Hudson, the three people Sherlock risked his life to save when he jumped off the roof of Bart’s. If you want some subliminal messaging that Sherlock was not protecting the shooter, but, as John said, ‘someone’, there it is. At the center of the shot is John, who then, of course, comes to a realisation: he’s sitting in my armchair. He then asks:

"Mrs Hudson, why did Sherlock think I’d be moving back in here?"

The realisation hits him then. Sherlock was not protecting the shooter. He was protecting his best friend.

Let’s skip along a little bit. Mary goes to Leinster Gardens, where Sherlock calls her. He brings her to his bolthole. How does he describe that bolthole?

"The empty houses."

Let’s take a look at an extract from The Adventure of the Empty House:

I had imagined that we were bound for Baker Street, but Holmes stopped the cab at the corner of Cavendish Square. I observed that as he stepped out he gave a most searching glance to right and left, and at every subsequent street corner he took the utmost pains to assure that he was not followed. Our route was certainly a singular one. Holmes’s knowledge of the byways of London was extraordinary, and on this occasion he passed rapidly and with an assured step through a network of mews and stables, the very existence of which I had never known. We emerged at last into a small road, lined with old, gloomy houses, which led us into Manchester Street, and so to Blandford Street. Here he turned swiftly down a narrow passage, passed through a wooden gate into a deserted yard, and then opened with a key the back door of a house. We entered together, and he closed it behind us.

The place was pitch dark, but it was evident to me that it was an empty house. Our feet creaked and crackled over the bare planking, and my outstretched hand touched a wall from which the paper was hanging in ribbons. Holmes’s cold, thin fingers closed round my wrist and led me forward down a long hall, until I dimly saw the murky fanlight over the door. Here Holmes turned suddenly to the right, and we found ourselves in a large, square, empty room, heavily shadowed in the corners, but faintly lit in the centre from the lights of the street beyond. There was no lamp near, and the window was thick with dust, so that we could only just discern each other’s figures within. My companion put his hand upon my shoulder and his lips close to my ear.

“Do you know where we are?” he whispered.

“Surely that is Baker Street,” I answered, staring through the dim window.

“Exactly. We are in Camden House, which stands opposite to our own old quarters.”

“But why are we here?”

“Because it commands so excellent a view of that picturesque pile. Might I trouble you, my dear Watson, to draw a little nearer to the window, taking every precaution not to show yourself, and then to look up at our old rooms–the starting-point of so many of your little fairy-tales? We will see if my three years of absence have entirely taken away my power to surprise you.”

I crept forward and looked across at the familiar window. As my eyes fell upon it, I gave a gasp and a cry of amazement. The blind was down, and a strong light was burning in the room. The shadow of a man who was seated in a chair within was thrown in hard, black outline upon the luminous screen of the window. There was no mistaking the poise of the head, the squareness of the shoulders, the sharpness of the features. The face was turned half-round, and the effect was that of one of those black silhouettes which our grandparents loved to frame. It was a perfect reproduction of Holmes. So amazed was I that I threw out my hand to make sure that the man himself was standing beside me. He was quivering with silent laughter.

“Well?” said he.

“Good heavens!” I cried. “It is marvellous.”

“I trust that age doth not wither nor custom stale my infinite variety,” said he, and I recognized in his voice the joy and pride which the artist takes in his own creation. “It really is rather like me, is it not?”

“I should be prepared to swear that it was you.”

“The credit of the execution is due to Monsieur Oscar Meunier, of Grenoble, who spent some days in doing the moulding. It is a bust in wax. The rest I arranged myself during my visit to Baker Street this afternoon.”

“But why?”

“Because, my dear Watson, I had the strongest possible reason for wishing certain people to think that I was there when I was really elsewhere.”

“And you thought the rooms were watched?”

“I knew that they were watched.”

“By whom?”

“By my old enemies, Watson. By the charming society whose leader lies in the Reichenbach Fall. You must remember that they knew, and only they knew, that I was still alive. Sooner or later they believed that I should come back to my rooms. They watched them continuously, and this morning they saw me arrive.”

The specific enemy in question, who Holmes and Watson apprehend, is Colonel Sebastian Moran, the late Moriarty’s right-hand man, described thus:

Moran, Sebastian, Colonel. Unemployed. Formerly 1st Bangalore Pioneers. Born London, 1840. Son of Sir Augustus Moran, C. B., once British Minister to Persia. Educated Eton and Oxford. Served in Jowaki Campaign, Afghan Campaign, Charasiab (despatches), Sherpur, and Cabul. Author of Heavy Game of the Western Himalayas (1881); Three Months in the Jungle (1884). Address: Conduit Street. Clubs: The Anglo-Indian, the Tankerville, the Bagatelle Card Club.

On the margin was written, in Holmes’s precise hand:

The second most dangerous man in London.

A trained assassin, currently unemployed, who Holmes and Watson confront in an empty house. Remind you of anyone?

Let’s add to that her very suspicious behaviour regarding apparently not recognising Sherlock on the day they met. May she, like Moran, have known that Sherlock was alive, and have been watching him?

Here, again, Sherlock demonstrates that he does not trust Mary: “Remind you of anyone, Mary? A façade?”

His later demonstration of apparent trust is most certainly an act.

Almost as soon as Mary enters the building, her hand goes to her gun:

She certainly doesn’t have any qualms with killing Sherlock. She confirms this herself not long afterwards:

MARY: “You were very slow.”

SHERLOCK: “How good a shot are you?”

MARY: “How badly d’you wanna find out?”

Now, of course she doesn’t then actually kill him - that would ruin the narrative; the shooting of the coin has to serve as a suitable alternative. She of course shoots it excellently. Now, here comes the odd bit:

SHERLOCK: “And yet over a distance of six feet you failed to make a kill shot. That wasn’t a miss. It was surgery. I’ll take the case.”

And yet, it wasn’t a miss. It was a very good shot. Sherlock died. So why say it? I’ll come back to that.

MARY: “What case?”

SHERLOCK: “Yours. Why didn’t you come to me in the first place?”

MARY: “Because John can’t ever know that I lied to him. It would break him and I would lose him forever, and Sherlock, I will never let that happen. Please, understand, there is nothing in this world I would not do to stop that happening.”

Like killing one of the most intelligent and observant men in the world who also happens to be his best friend, for instance? Your selfishness is showing again there, Mary.

Now let’s take a look at the confrontation between Sherlock, John and Mary back in 221b:

JOHN: “You… What have I ever done? Hm? My whole life… to deserve you.”

SHERLOCK: “Everything.”

JOHN: “Sherlock, I’ve told you… Shut up.”

SHERLOCK: “No, I mean it, seriously, everything. Everything you’ve ever done is what you did.”

JOHN: “Sherlock, one more word and you will not need morphine.”

SHERLOCK: “You’re a doctor who went to war; you’re a man who couldn’t stay in the suburbs for more than a month without storming a crack den, beating up a junkie. Your best friend is a sociopath who solves crimes as an alternative to getting high. That’s me by the way - hello! Even the landlady used to run a drug cartel. […] John, you are addicted to a certain lifestyle. You’re abnormally attracted to dangerous situations and people. So is it truly such a surprise that the woman you fall in love with conforms to that pattern?”

JOHN: “But she wasn’t supposed to be like that! Why is she like that?”

SHERLOCK: “Because you chose her.”

At first, this seems cruel. It seems as though Sherlock is forcing the blame of the situation on John, and certainly, that’s how John takes it - “Why is everything… always… MY FAULT?”

However, might this not be more evidence for the Mary-as-Moriarty’s-ex-right-hand-(wo)man theory? She’s not dangerous because John chose her or vice versa, but she put herself in John’s path because he’s caught up in that dangerous lifestyle, and with Sherlock.

She is, after all, a nurse, and does that suit her? Presumably she’s taken innocent lives. If she had only taken the lives of bad people, why would John care? He’s done exactly the same, as she presumably knows - he was, after all, in the army in a protective role. Mary is not an altruist. She does not have a personality suited to nursing. She presumably trained as a nurse during her five years since taking Mary Morstan’s identity, too, and not an NHS nurse, either - she works privately at John’s clinic. Less background checks, then. It seems to me that Mary intentionally put herself in John’s path. The Moriarty connection is looking likelier and likelier.

Let’s go a bit further.

SHERLOCK: “John, listen, be calm and answer me. What is she?”

JOHN: “My lying wife.”

SHERLOCK: “No, what is she?”

JOHN: “And the woman who is carrying my child who has lied to me since the day I met her.”

SHERLOCK: “No. Not in this flat, not in this room, right here, right now, what is she?”

JOHN: “Okay. Your way. Always your way. Sit.”

MARY: “Why?”

JOHN: “Because that’s where they sit! The people who come in here with their stories. The clients - that’s all you are now, Mary. You’re a client. This is where you sit and talk and this is where we sit and listen. Then we decide if we want you or not.”

In this scene, John completely places his trust in Sherlock and disowns Mary. He also mentions that she is carrying his child. Let’s continue.

Mary hands John a memory stick:

SHERLOCK: “A.G.R.A. What’s that?”

MARY: “My initials. Everything about who I was is on there.”

Oh, really? You said you would do anything to prevent John from finding out the truth about you, and yet you just happened to be carrying all of the information about your past with you?

Liar.

For those of you who aren’t away, the initials are a reference to a Great Agra Treasure of The Sign of Four, which turns out to be missing, the case empty:

“That is all over,” I answered. “It was nothing. I will tell you no more gloomy details. Let us turn to something brighter. There is the treasure. What could be brighter than that? I got leave to bring it with me, thinking that it would interest you to be the first to see it.”

“It would be of the greatest interest to me,” she said. There was no eagerness in her voice, however. It had struck her, doubtless, that it might seem ungracious upon her part to be indifferent to a prize which had cost so much to win.

“What a pretty box!” she said, stooping over it. “This is Indian work, I suppose?”

“Yes; it is Benares metal-work.”

“And so heavy!” she exclaimed, trying to raise it. “The box alone must be of some value. Where is the key?”

“Small threw it into the Thames,” I answered. “I must borrow Mrs. Forrester’s poker.”

There was in the front a thick and broad hasp, wrought in the image of a sitting Buddha. Under this I thrust the end of the poker and twisted it outward as a lever. The hasp sprang open with a loud snap. With trembling fingers I flung back the lid. We both stood gazing in astonishment. The box was empty!

No wonder that it was heavy. The ironwork was two-thirds of an inch thick all round. It was massive, well made, and solid, like a chest constructed to carry things of great price, but not one shred or crumb of metal or jewellery lay within it. It was absolutely and completely empty.

“The treasure is lost,” said Miss Morstan calmly.

I don’t think that that memory stick contained the truth, the whole truth and nothing but the truth, do you?

Then let’s look at this speech of Sherlock’s:

"By your skill set, you are or were an intelligence agent. Your accent is currently English but I suspect you are not. You’re on the run from something. You’ve used your skills to disappear, Magnussen knows your secret, which is why you were going to kill him, and I assume you befriended Janine in order to get close to him.”

'Are' is not looking likely. Look what MI6 has to say about that role:

'What about secrecy? Well obviously the details of your work will be secret and we ask you not to discuss your application with anybody. That said, once you join us you'll be able to disclose your role to one or two close friends or family. We'll help you create a credible cover story for everyone else.'

So why haven’t you disclosed your role to John, Mary? Where’s your credible cover story? No, she’s not an intelligence officer anymore.

She has disclosed her role to someone, though. Remember how quickly she said “Oh, he would have needed a confidante!” in reference to Sherlock going on the run? You’re on the run too, Mary. Who’s your confidante?

Then there’s this:

MARY: “The stuff Magnussen has on me - I would go to prison for the rest of my life.

JOHN: “So you were just gonna kill him?”

MARY: “People like Magnussen should be killed, that’s why there are people like me.”

JOHN: “Perfect. So that’s what you were? An assassin? How could I not see that?”

MARY: “You did see that. And you married me. Because he’s right. It’s what you like.

She’d go to prison for the rest of her life? Not if she was still with the secret service. She worked for much nastier people than that.

Here we also see another nasty trait of Mary’s come to light: she’s emotionally abusive. She turns the blame of the situation away from herself and onto John. She did say she’d do anything to prevent him from leaving her.

Look at John’s face, how he responds:

He is devastated, furious, he certainly doesn’t look like he plans to forgive her. So why do we see him do exactly that?

Well, for one thing, she’s carrying his child. He evidently cares about that - when she falls unconscious, he says to Sherlock: “Did you just drug my pregnant wife?” Emphasis on the ‘pregnant’.

For another, Sherlock tells him to: “John, John! Magnussen is all that matters now. You can trust Mary. She saved my life.”

Prior to that, he claimed that she fired “One precise shot to incapacitate [him] in the hope that it would give [her] time to negotiate [his] silence.” Yet again, she quite literally killed him. There is no proof that she really did call an ambulance, either - the scene in which we see her doing so is a reconstruction of Sherlock’s claim, and I used to have a horse. I saw lots of accidents. Multiple people would call an ambulance, and upon doing so, later people to call would be told that an ambulance had already been sent out to that particular incident. That didn’t happen to John. Perhaps there was good traffic that day, or an ambulance happened to be in the area. Besides, Sherlock fell unconscious within three seconds, went into shock (which can cause memory loss) and was dosed with morphine (which causes disorientation). Hardly the right circumstances to provide for a thorough analysis of the situation.

So why does Sherlock insist that Mary is trustworthy when he quite obviously doesn’t trust her? My guess is that he wants to placate her. He does, after all, say this in her presence. He wants to lull her into a sense of false security. We know that he wants what Magnussen has on her - “I want everything you’ve got on Mary”; “In return for the password, you will give me any material in your possession pertaining to the woman I know as Mary Watson” - but we don’t know why. Is it really to protect her? Or is it because he wants to know her secret?

John may be in on that - after all, he and Mary did undergo “months of silence”, and the timing of their ‘reconciliation’, just before the drugs took effect and everyone fell unconscious, was fortunate. I’m sure Sherlock invited John AND Mary to Christmas dinner for a reason. Perhaps John is just burdened by guilt and a sense of duty, and really is trying to forgive her, but the evidence suggests that he’s highly suspicious of her, too.

There’s also the fact that, when reconciling with her, he says “I’ve thought long and hard about what I want to say to you. These are prepared words, Mary. Chosen these words with care.” He also later says “I am very pissed off and it will come out now and then.”

John is not a good liar. Sherlock established this in The Empty Hearse:

JOHN: “One word, Sherlock, that is all I would’ve needed! One word to let me know that you were alive!”

SHERLOCK: “I’ve nearly been in contact so many times but I worried that, you know, you might say something indiscreet… You know, let the cat out of the bag.”

Now, nobody sounds natural when they speak from rehearsal. John’s repeated claim that that is what he’s doing, as well as letting Mary know that he will lose his temper with her in the future, is the perfect cover for an act by a not particularly good actor.

The editing of this section is important, too. It cuts between the confrontation scene in 221b and the reconciliation scene. That, to me, suggests that we are not supposed to buy into John’s forgiveness. It’s hard to, when we’ve just seen him so devastated and fuming.

So, onto the Magnussen scene. He really solidifies my theory that she was in cahoots with Moriarty. Let’s look at some of the things he says about her:

"I’m not a murderer, unlike your wife.”

'Murderer' is an interesting choice of word. It suggests worse than working with the secret service. If that was all he meant, presumably he would've said 'killer'. There are implications behind the word 'murderer' - implications of immorality.

"Oh, she’s bad, that one. So many dead people. You should see what I’ve seen."

Again, suggestions of immorality.

And my favourite:

"All those wet jobs for the CIA. Ooh! She’s gone a bit freelance now, bad girl. [laughter] Oh, she’s so wicked. I can really see why you like her.”

She clearly worked for someone who was not at all moral. Again, my bets are on Moriarty.

So why did Sherlock shoot Magnussen?

Well, let’s take a look at his expression upon discovering that Magnussen apparently keeps all of his blackmail material in his mind:

He looks horrified. Why? Because he cannot obtain the information and hence protect Mary? Or because he cannot obtain the information and hence learn her secret and hence protect John?

Then let’s consider what Magnussen says to John shortly before Sherlock shoots him:

"I know who Mary hurt and killed. I know where to find people who hate her. I know where they live. I know their phone numbers. All in my mind palace. I could phone them right now and tear your whole life down. And I will. Unless you let me flick your face."

After that, killing Magnussen seems to be Sherlock’s safest bet at protecting John. Mary may well be a risk to him, but so are all the people who hate her. John would be be fighting a war on two fronts if Magnussen set Mary’s enemies on her.

Then there’s the fact that Mycroft’s present (and in control). I think Sherlock suspects that Mycroft would protect him, and therefore allow him to continue to protect John. After all, as he said at the cottage: “Your loss would break my heart.” Indeed, he immediately commands: “Do not fire! Do not fire on Sherlock Holmes! Do not fire!”

In fact, I believe that Mycroft is the hero of this story.

Earlier on, at the cottage, he said to Sherlock:

"I have, by the way, a job offer I should like you to decline. […] MI6. They want to place you back into Eastern Europe. An undercover assignment that will prove fatal to you in, I think, about six months."

This is, of course, the assignment that Mycroft arranges for Sherlock to be sent on rather than being sent to prison for killing Magnussen. Now, would Mycroft do that without a plan? Would he really rather send Sherlock to his death than have him in prison? After all, “There will always come a time when we need Sherlock Holmes.”

Remember, too, how much Mycroft knows. He’s more intelligent than Sherlock, and Sherlock invited Mary to the family home when Mycroft was there. I suspect that Mycroft is well aware that something is up with Mary.

So, what does he do? Stages Moriarty’s resurrection. Brings back Sherlock, and, if Mary was in cahoots with him, smokes her out (she does sound suspiciously tense upon being told that Moriarty is still alive). Kills two birds with one stone. Yes, he reacts with surprise to the news, but he does so over the phone. He could very well be acting. He responds very calmly, after all.

I think Sherlock was counting on Mycroft. This dialogue is very suggestive:

JOHN: “The game is over.”

SHERLOCK: “The game is never over, John. But there may be some new players now. That’s okay. The east wind takes us all in the end.

JOHN: “What was that?”

SHERLOCK: “It’s a story my brother told me when we were kids. The east wind, this terrifying force that lays waste to all in its path. Seeks out the unworthy and plucks them from the earth.

Are you expecting the east wind to pluck Mary from the earth, Sherlock?

Then, when Mycroft calls Sherlock and asks how his exile is going, he replies “I’ve only been gone four minutes.”

We’ve seen him pass comment on Mycroft’s timing before - in the Baskerville labs in The Hounds of Baskerville and in Mycroft’s office in The Empty Hearse. Was he expecting to return? Quite possibly. So soon? Possibly not.

Perhaps Mycroft’s not slipping as much as Sherlock thinks he is.