For whatever reason, this was the cap that made it all make sense to me.
I just rewatched HLV, and during the shooting-Sherlock scene I decided to watch Magnussen instead of Mary. Consequently, I noticed this: while Mary is distracted by Sherlock, Magnussen is leaning over. This particular cap comes from somewhere in the middle of the “shoot them both and leave” scenario during Sherlock’s explanation to John of his shooting, but I only picked it because it shows Magnussen most clearly. If you watch carefully, you’ll see that he does this in every iteration of the shooting, be it hypothetical, recapitulated, or the event itself.
Whachu doin, Magnussen?
To answer that, we need a wider shot of the room. This one comes from Sherlock’s recap of Mary shooting him, but again, I chose it for the sake of clarity. The element I want to address appears in every iteration.
What’s that little black square on the carpet, Magnussen? A phone? Conveniently within your reach, is it not? Of course, you’d have to lean over to get to it.
[[EDIT: CONFIRMED that the black square on the floor of Magnussen's bedroom is indeed a phone. It's the same one, in fact, that Mary uses to phone 999 in Sherlock's recap of events. If you watch carefully, you'll see that after she strikes Magnussen, she leans down to the same place he was leaning, picks up a phone, and dials.]]
Now, Sherlock said that, if calling the ambulance had been left to John, he would have died. He uses this as justification for saying Mary called the ambulance. But what if it wasn’t Mary who dialed 999 — what if it was Magnussen?
He was being threatened. Someone had broken into his office (bedroom??) and now held a gun to his head. When we first see him, he’s trying in vain to negotiate with Mary. But in comes Sherlock, and Mary is diverted, giving Magnussen time to reach for his discarded phone.
If Magnussen called the police, this tells us something very important about Mary. Namely, that she never intended for Sherlock to survive getting shot.
Now, I already had the idea in my head that she meant to kill Sherlock, for the reasons that a) in his mind palace, Sherlock continuously refers to the inevitability of his own death, and b) I read someone else’s brilliant meta a while back describing (with diagrams!) exactly where the bullet hit and exactly how lethal the shot actually was. (
If anyone knows which meta I’m talking about, please let me know so I can add a credit here! You'll find said credit in the notes at the end.) So Sherlock’s survival in this instance was an accident, aided by Magnussen’s call and Sherlock’s own determination to live.
She wanted him silent, obviously, but if her motive really was as innocent as she claims, she didn’t need to shoot Sherlock to shut him up. It’s at this point, when she’s cast in a suspicious light, that she should logically tell Sherlock the truth and ask for his trust. But she doesn’t trust him; she doesn’t even try. She shoots him in the chest. This begs the question: Why did Mary want Sherlock dead? Or, if his death was merely incidental, why did she seem to have no qualms about killing him?
I’ve latched onto the theory that Mary is Sherlock's Moran. She's great with a gun, no? Supposedly she was a CIA assassin; it's more than likely she's learned how to handle a sniper rifle. ACD's Moran was “the best heavy-game shot that our Eastern Empire has ever produced,” according to “The Empty House.” Moran also was a military man — a killer working for the government — until he retired, and was then picked up by Moriarty. While Magnussen is rifling through her mental file in Appledore towards the end of HLV, he mentions that “she's gone a bit freelance now. Bad girl.” She's left the government, and at this point she's likely started working for Moriarty. Speaking of empty houses, Sherlock's “empty houses” where he arranges to meet with Mary both draw our attention back to Mary's deception and subtly pull the thread of “The Empty House” through from the beginning to the end of series 3. I read this as a possible suggestion that elements of that story are still relevant, and more specifically, that Mary Morstan is this Holmesian iteration's Sebastian Moran. (Additionally, a somewhat minor note: she does the lizard thing. The reptilian head-bobbing thing. Moriarty does it all the time, and was described as doing it in ACD canon. This one little tic, which Moftiss describe in the commentary of (I think) TGG as being totally intentional, is shared by both characters, and maybe it's not a coincidence.)
[[EDIT: I think Sherlock had an inkling of this, too -- that Mary is Moriarty's fabled second-in-command. In his mind palace again, as he's lying in the hospital bed, he interrogates his mental Mary
and he's thinking, he's thinking...
and then: epiphany. And we cut from Sherlock's epiphany face
to Mary's gun.
Now, there are many things this could mean, but my guess is that one of those possibilities includes Sherlock making the connection between Moriarty's master gun(wo)man of a second officer and Mary's precision with a handgun.]]
So, if Mary is allied with Moriarty, why is she now married to John? Magnussen kindly laid out the path for us here: “Mycroft’s pressure point is his junkie detective brother, Sherlock. And Sherlock’s pressure point is his best friend, John Watson. John Watson’s pressure point is his wife. I own John Watson’s wife, I own Mycroft.” (If Moriarty really was alive on that rooftop, he had to have seen Sherlock fake his death, and if he didn’t, the sniper who’d been targeting John certainly did. We can probably assume Moriarty knows Sherlock’s alive.) So if we assume Mary operates according to Moriarty’s orders, then we can safely say that she pursued John so that Moriarty would have a (wo)man on the inside, one that would then open up the path to Mycroft, “the most powerful man in the country.” Moriarty has Mary, he has John; he has John, he has Sherlock; he has Sherlock, he has Mycroft; and if he has Mycroft, Moriarty has England.
But Moriarty and Mary aren’t the only ones who want power over the country — Magnussen wants it, too. He’s a competitor. And somehow, Mary was driven to threaten him at gunpoint. Why? Well, here’s where I’m gonna give Mary some credit: I think she really does love John. She pursued him because she was ordered to (and really, how likely was it that John would happen to take up with, propose to, and marry a CIA assassin? Even if it is “what he likes” — all the women in London, and he happens upon the one with a license to kill). But somewhere along the way, she saw him for what he is: brave, kind, wise, loyal John. So now John has become her pressure point, and Magnussen knows it — “Oodles of love and heaps of good wishes from CAM. Wish your family could have seen this.” — and he plans to use it against her. (Conjecture: Magnussen had something to do with whatever happened to Mary’s family, too. Add old resentments to the list of reasons Mary has to threaten him.) So Mary goes to Magnussen’s office with the dual motives of protecting Moriarty’s operation and protecting John from learning the truth about her. Maybe she thinks that, when all is said and done, and as long as Magnussen doesn’t fuck it all up, she’ll have a chance to assume Mary Morstan’s identity permanently, and live out her days with our lovely John.
But then Sherlock shows up, so Mary has to change her game plan. Her original intention was only to threaten and probably kill Magnussen. That’s off the table — as Sherlock says, if Mary killed Magnussen, John would be suspect. She knows he’ll stay silent, though, if only she can get out of this room, so while her initial problem will be left unresolved, no new damage will be done by leaving Magnussen still breathing. Sherlock is another matter. His seeing her in this context means that he knows she isn’t who she says she is, and it means he’ll probably figure out the whole truth eventually. Simplest way to prevent that is to shoot him, so she does. His survival is an unexpected snag, but she can’t just go and shoot him again, tempting though it may be with him lying vulnerable in a hospital bed. Too many potential witnesses, too many questions. So she lets him live, but threatens him not to tell John. She’s probably trying to think up some alternative way of keeping Sherlock quiet, but, as it turns out, Sherlock helps her with that. Finally, we turn to him. How much does he know? And how much does he actually say?
He says Mary’s shot was “surgery.” He probably doesn’t believe this. Every person in his mind palace was telling him he was “most certainly going to die,” that he’d been murdered. His heart stopped. And I think that if Magnussen really was the one to phone 999, Sherlock would have seen it — it was in his direct line of sight, after all, and Magnussen’s little lean appears in every iteration of the shooting, including Sherlock’s own retellings. I think he knows Mary set out to kill him when she pulled the trigger. I think he also knows Mary genuinely cares about John — “I’m sorry, Sherlock. I truly am,” she says, perhaps feeling guilty about putting John through Sherlock’s death a second time — and so, with John in the room watching, Sherlock casts her attempt at murder as her saving his life. He tells John that she phoned the ambulance, too. He’s protecting John. He’s helping Mary.
But maybe he’s not just helping her out of the kindness of his heart. I think that, after all this, he suspects that there’s more to Mary than just a troubled past. Now that he knows what she’s done and what she’s capable of, he may be wary of her involvement in John’s life in the first place. But he doesn’t want to hurt John before he knows for sure; furthermore, it might cause a permanent rift in their friendship if it looks like Sherlock is trying to drive a wedge between John and his wife.
Then Mary does this:
The AGRA files. The magical answer to it all. Mary’s been lying about her identity this whole time, but don’t fret! She just so happens to have her entire life story on a USB, and she’s carrying it with her right now! Yeah, okay. In The Sign of Four, as has already been pointed out by many others, but as I will reiterate here, Agra was a place in India where a great deal of treasure had been hidden. They eventually found the place empty. I think it’s pretty likely that this USB is empty. But Mary shows it to John because she needs him to trust her.
She shows it to Sherlock, too. Now, Sherlock is being quite admirably respectful of John’s power to choose his next move in this whole scenario — John’s wife, John’s life, John’s decision. During this conversation, Sherlock is mostly there to facilitate the exchange of information, and otherwise he backs off. But even with all this newfound consideration, here, lying in front of him, is a single memory stick that holds the answers to every one of his questions. Sherlock knows about the AGRA files for months before John burns them. Do you think he’d ignore them for so long? I don’t. I think he folded. I think he peeked. And I think he found them empty.
Now he knows something is wrong. John Watson is definitely in danger. So what does he do? Sherlock being Sherlock, he does all he can to learn about Mary’s past, but you can imagine how many dead ends he runs into. Of course, he knows one person who’s got a whole file of Mary tucked away in a vault. Magnussen is Sherlock’s last resort.
I don’t think Sherlock would have put the security of an entire country in jeopardy for the sake of protecting Mary and/or John. He’s not a sociopath, despite what he says, but he is a rational man, and putting so much power in the hands of a blackmailer in order to prevent some hypothetical blackmail would be a pretty stupid move. But Sherlock’s on a different scent now; he suspects that Mary is far more dangerous and that the danger is far more immediate than she would have them believe. We got this little tease at the beginning of the episode, and I’d like to jump back to it now:
"Information is the power to change." Information is power, and it’s Sherlock’s weapon of choice. He needs information on Mary, and he knows where to get it. So he goes to Appledore under the pretense of protecting Mary and John, with the added bonus of getting a dangerous man — and, it’s worth noting, perhaps the only person Sherlock Holmes hates unambiguously — put behind bars.
"I want everything you’ve got on Mary," he tells Magnussen. But Magnussen, as it turns out, doesn’t have anything. To get the information out of him, Sherlock would have to interrogate him, and he could never trust the information he got. This lead is a dead end. He still doesn’t know who Mary was, or who she is, or what she’s doing with John. But he knows she’s a liar.
Magnussen now presents a problem. Because there are no vaults, there can be no arrest. Magnussen has the power to tear Mary and John’s life apart. And he’s also made more than one allusion to dominating on a greater scale: “This is what I do to whole countries,” he says, and back in Baker Street, “If it works here, I try it in a real country.” Even if he says he has no “evil plan,” Magnussen is slowly working his way up the ladder on a global scale. He’s nearly got the British government in his pocket, the laptop Sherlock helpfully provides being key in his total domination of the United Kingdom; he alludes to the intent to expand his web beyond British borders. Magnussen may be no friend of Mary’s, but he’s dangerous in his own right, and Sherlock must realize that even if his brother confiscates the laptop, Magnussen will continue to cripple the western world, and the destruction he could wreak is unimaginable. So, his previous plan thwarted, Sherlock gives in to desperation, dissolving Magnussen’s power with a single bullet to the head. He’s protecting the world from Magnussen’s wrath, and he’s protecting Mary’s identity, but he’s also buying himself time to figure out who she is and why she’s there.
So we’re done with Magnussen now, but we’re far from done with Mary. Even after John puts the issue of Mary’s past to bed, Magnussen dredges it all up again. “Oh, she’s bad, that one. So many dead people. You should see what I’ve seen.” This vein is left wide open and unresolved. I suppose we’ll see what happens with Mary in series 4.
This is quite a lot of information, I know, and a lot of conjecture. Please let me know if there’s something I’ve missed/something I haven’t sold you on. Let’s talk it out! Mostly I just really want to understand what the hell is going on.