This meta covers:

AGRA are not Mary’s initials. AGRA are the people after Mary who want to hurt her. The flash drive contains false information.

Jim made the flash drive and the lies on it. The punctuation is a clue.

In the season three DVD commentaries, Steven Moffat said that what was actually on the flash drive was five episodes of Doctor Who. While this is obviously false, the fact that he brought it up at all - and said what was on it - probably means that the narrative isn’t done with the flash drive and Moffat thinks you should be curious as to what’s on it. There’s definitely more to the flash drive than the obvious.

So what the hell could be on that flash drive … and what the hell is AGRA?



First off, I don't think AGRA is Mary’s initials:

Mary puts the flash drive on the table; Sherlock immediately asks about AGRA:

Mary looks a bit deer-in-the-headlights, which is very much not her:

Then, for the only time in the whole conversation - the only time in the whole season - Mary hesitates and stutters over her words:



She’s lying. AGRA aren’t her initials, and what’s more, Sherlock knows it:

He purses his mouth and looks away. She’s lying and he knows it.



It’s way more obvious in the video, take a look:



source



Possibilities about what Mary’s hesitation over AGRA could mean:

It’s a double bluff. AGRA are her initials and she’s trying to pretend like she’s more nervous than she is to get John to feel sorry for her. But since it’s the only time she does this in the whole conversation, it doesn’t seem like her plan is to seem worried and upset. It’s a lie. Sherlock knows/suspects what AGRA stands for and he asks Mary to check how much she’s going to lie. He looks away and purses his mouth after she says it - he totally knows/deduces she’s lying. It’s a terrible lie: she does like five lying tells.

I’m pretty sure Sherlock has heard of AGRA before he met Mary because of the way he zooms in on the flash drive. It seems really likely he heard about it when he was away, and the one place we see him is Serbia – a country in which they use Cyrillic, the alphabet that CAM’s documents about Mary are in.



It also just doesn’t make sense for her to write her initials on the flash drive. There’s no risk to putting her initials on it, particularly if it’s only about CIA stuff or blank or something, right? Wrong. The CIA knows she went freelance. If those are her real initials, it would be easy for Mycroft to call up the CIA and ask for information on an agent with the initials AGRA. For all Mary knows, the CIA would say “Yeah, she used to work for us, but she went rogue during this mission that we think had ties to Jim Moriarty. You’ve found her?”

Giving Sherlock, John, and Mycroft her real initials gives them an opportunity to access way more information than she clearly wants them to have. Before being willing to talk to Sherlock, Mary asks him how much she already knows, obviously so she doesn’t accidentally tell him anything else:

MARY: How much d’you know already?

SHERLOCK: By your skill set, you are – or were – an intelligence agent … (x)



She’s clearly not willing to volunteer additional information about herself, so it makes no sense that she’d volunteer her real initials. So I don’t think those are Mary’s initials at all.

Mary’s actual real name>>



Possibilities of what’s on the flash drive:

a) Everything she’s ever done. Well, no one puts a list of all their hits and work for Jim on a flash drive. How stupid do you think Mary is? Even if she’s a good guy, no one puts a list of all their hits on a flash drive, lets it out of their sight for six months, and labels it with their initials. What if John lost it? What if it was stolen from him?



b) Nothing. Possible, but unlikely because - though Mary suspects John won’t read it - she can’t be sure. If John reads it and finds nothing, he’s definitely leaving her. Why would she risk giving him a blank flash drive? And if it was blank, why would she write AGRA on the front? It’s not like someone would expect her to have her initials on the outside of a flash drive about her hits. It wouldn’t be suspicious at all if the outside of the flash drive was blank, so why write anything on the outside?



c) Just her work for the CIA. It seems like this would be a good thing to put on there: enough truth that John would buy it, but not so bad that he’d leave her. But there’s a problem. John won’t contact the CIA to check up on this, but Sherlock and/or Mycroft definitely will. The CIA knows she went freelance. So they might a) tell Sherlock and Mycroft way more stuff than Mary wants them to know and b) come and arrest Mary.

d) Her childhood before she joined the CIA. Again, Sherlock and/or Mycroft are definitely going to contact the CIA. (“Tell me about a recruit from Virginia born 1979… Oh, she went rogue during a mission you think had ties to Jim Moriarty?”)

Basically, if Mary gives them any real information at all, there’s a good chance they will be able to find out everything, and Mary obviously doesn’t want that. It’s not 100% Sherlock and Mycroft would be able to figure out everything based on scraps of real information, but if I were Mary, I really, really wouldn’t take that chance. Which brings us to:

e) Lies. Totally fake information about working in the CIA. John wouldn’t know it’s a lie, but Sherlock or Mycroft would be able to figure it out. If they call up the CIA and ask about an agent who did these six things, and the CIA never had an agent matching that description, it’s obviously a lie. But they still won’t be able to find out anything else about her, so she’s safe. So I think it’s all lies.

(If you’re thinking the AGRA box in ACD is empty, I’d say filling the flash drive with lies qualifies as “empty.” It’s still empty of anything useful. Even if it actually is blank, which is possible, it doesn’t really matter: it’s either lies or it’s blank, and either way, the point is that it’s got nothing helpful on it about Mary.)

I don’t think Mary made that flash drive. I think Jim did:

1) Mary hesitates telling Sherlock and John what AGRA stands for. What if it’s because she really doesn’t know?

2) Jim is the master of faking identities. Jim could definitely concoct a believable lie about Mary’s work for the CIA. Most people - including Mary, probably - would find that very difficult. But we know Jim can come up with a fake backstory that holds up for at least a while.

3) I am in no way a handwriting expert, but these look kind of similar to me. Jim had the same person write them? (Possibly Mary? Even more likely: Janine?)

4) Here’s the big one: Mary volunteering the flash drive is so OOC. The more I think about this, the more convinced I am. It makes total sense that Mary would rather write down the information rather than talk it out with John: she’s even worse at emotional things than John is. So her giving them the flash drive isn’t OOC, but her volunteering it is. It’s easy to miss that this is what happens because it’s right at a transition from the Watsons Have A Domestic to Christmas. But giving them the flash drive is the very first thing she does - the very first thing anyone does - when they sit down in their chairs. John doesn’t ask for it. Sherlock doesn’t ask for it. John doesn’t even ask about her past. No one even knows that she has this flash drive. No one has said anything, and she just hands it over immediately. This makes no sense. No one would do that, especially not Mary. Here’s why:

a) John isn’t even really interested in her past at the moment. He’s a) only speaking to Mary at the moment because Sherlock told him to; and b) much more interested in her shooting Sherlock than her shooting random other people. They only get onto the assassin topic because Mary gives them the flash drive. So John wouldn’t have asked for this sort of information, at least not then. She could’ve kept quiet.

b) Mary never gives more information than she has to: she had the time Sherlock was in the hospital (at least the time it takes for Janine to publish the newspapers) to tell John she was the one who shot him herself - it would’ve been the smart move because it’s a pretty good guess Sherlock’s going to tell him eventually, and it’ll look better for her if she tells John herself - and she doesn’t. She doesn’t volunteer information. Before being willing to talk to Sherlock, Mary asks him how much she already knows, obviously so she doesn’t accidentally tell him anything else:

MARY: … and I don’t want to see that happen.

(She looks down. With a loud sigh John snatches the drive from the table, looks briefly across to Sherlock and then shoves the drive into his left trouser pocket.)

MARY: How much d’you know already?

SHERLOCK: By your skill set, you are – or were – an intelligence agent … (x)



She’s clearly not willing to volunteer additional information about herself, so why give them the flash drive? It makes no sense with what she says in a moment - “How much d'you know already?” - because that clearly implies she’s not going to tell them anything they don’t know. But theoretically, the flash drive tells them everything about her. Those two actions - “How much d'you know already?” and volunteering the flash drive - are totally contradictory.

c) The smart move, if John asked her about her past - which again: he doesn’t - would’ve been to say that she’d give him all the information, but it was at home, so she’d give it to him the next day. That would’ve given John some time to calm down.

d) Why does she even have this flash drive - theoretically with info that would send her to prison for the rest of her life - just casually on her person? She didn’t intend for John to find out she was an assassin when she went to The Empty House, so she didn’t bring it for him. Literally, why does she even have it? Why did she decide to bring a flash drive to The Empty House to meet Sherlock? She definitely didn’t think she was going to give Sherlock her case, so she didn’t bring the info for him. The fact that she brought it tells us that giving it to John was a prearranged plan. But she never thought John would find out she’s an assassin, so why would she have made this flash drive? So she didn’t make the flash drive - since she didn’t think John would find out she was an assassin and therefore she wouldn’t ever need it - so she must’ve gotten it from someone else.



e) Giving John information on her is admitting that John has some power over her. It’s admitting that she needs to justify her actions to him in some way, and she doesn’t think that, not just about the assassin/shooting Sherlock thing, but ever. It’s why she doesn’t even try to lie and tell John she’s sorry for shooting Sherlock - it would’ve been by far the smartest thing to do, even if it was a total lie. Mary will not give at all in an argument. She’s very much into ultimatums: this is me, and if you don’t like it, get out. We know she’s desperate to keep John, and even then, she can’t manage to swallow enough pride to lie and say she’s sorry, either for shooting Sherlock or for lying. She will not back down, ever. We got an example of this when she shot Sherlock. She told him if he took another step, she would kill him: he did, so she did:

But giving John the flash drive is a compromise - even if small - with him. Mary would just say, “No. This is just what you like. You married me. End of story. I don’t owe you anything.”

The fact that giving them the flash drive is her immediate reaction makes it look like it was her plan all along. But like I’ve said, it being her plan doesn’t make any sense. So what if it was someone else’s idea? Mary doesn’t trust Jim, but she’s just learned that John is more loyal to Sherlock than to her, so she’s siding with the lesser of two evils, in her mind.

So here’s the theory:



Two years ago, when Mary went undercover with John after Reichenbach, Jim gave her this flash drive and said “If your cover’s ever blown, tell John to read this flash drive and it will explain everything away.” So Mary popped it in her computer and checked it out. It showed a great lie about her work for the CIA. Perfect. Fast-forward two years to when Mary’s cover is blown. She doesn’t trust Jim at this point because she realized he screwed her over when Sherlock showed up in CAM’s office. But when Jim gave her this two years ago, they were tight, and plus Mary knows what’s on it. So she hands it over to John.

There’s no way Jim could predict two years into the future, right? He probably could, but the thing is: he doesn’t have to. He knew when he gave the flash drive to Mary that Sherlock wasn’t dead, and he knew Mary’s cover wasn’t going to be blown until Sherlock returned; John wasn’t going to figure it out. In fact, it wasn’t blown until Jim let it be blown, so he would have a good guess at what the circumstances would be, even two years previously. And even if he didn’t, it doesn’t matter. That flash drive isn’t for John; it’s for Sherlock. It’s information Jim wants Sherlock to have. The flash drive is a clue to Sherlock from Jim in addition to Mary’s fake CIA information - and the clue is the punctuation.



Here’s what the punctuation of AGRA reminds me of:

There’s a dot after the I and not after the O or the U. Several letters, one dot.

There’s a dot of after the A and the G, but not after the R or the A. Several letters, two dots.

Counting up? Or alternately: both have two dots missing.

So perhaps Jim is doing another version of The Five Pips, but “for real” this time.

If AGRA aren’t her initials, then what is it?



A project? A person’s initials? A list? An organization?



CAM’s documents (with AGRA on them) about Mary are in Cyrillic, which is the alphabet used in a lot of other countries in Eastern Europe, which is definitely a theme.



AGRA is not a word in any language except Italian, where it means sour. So AGRA must stand for something.



It doesn’t seem like Mary can actually know what AGRA really is: she’s got to just think that it’s her fake initials. Because if she knows what it really is – if it’s a project she was involved in, for example – she wouldn’t put it on the outside of the flash drive. Jim made the flash drive and wrote AGRA on the outside, but if Mary knew what AGRA really was, she’d say: “Jim, what are you doing? You said this flash drive would tell a good lie and make all John’s suspicions go away. Putting the real project on the outside won’t do that.” So then she wouldn’t give them the flash drive. Mary would know that any real information – particularly something big like a project name – could easily be traced back to the agents who worked on it, and then it would be easy for Sherlock and Mycroft to find out everything about her.

But because CAM’s documents show AGRA with Mary’s picture next to it, AGRA and Mary have to be connected. So AGRA is something that’s connected to Mary that Mary doesn’t know about, at least not by that name. That doesn’t seem like it could be a project she worked on: she must know all the names of the project she worked on. Same with an organization she was in.

We know from CAM’s documents - with AGRA written on them - that he has information on Mary. And what does CAM threaten Mary with? People who want to hurt her. He doesn’t threaten to turn her into the CIA or the police, which would probably be easiest. But he doesn’t actually intimate that he has very specific information on what she’s done: he says she’s an ex-CIA agent who went rogue. That’s pretty vague. But apparently he has very specific information on who wants to hurt her: he says he knows their names and phone numbers:

MAGNUSSEN: It works like this, John. 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. (x)



He doesn’t have the phone numbers of people she’s killed because they’re now dead and don’t have phones. So the information he’s got has to be on the people who hate her. And the information he’s got is AGRA. So I think AGRA is the people who hate her.

This is a direct tie-in to The Valley of Fear (I think Mary is both Birdy Edwards (the main character in The Valley of Fear) and Sebastian Moran):



The sergeant picked up a card which lay beside the dead man [Birdy Edwards] on the floor. The initials V. V. and under them the number 341 were rudely scrawled in ink upon it. “What’s this?” he asked, holding it up. Barker looked at it with curiosity. “I never noticed it before,” he said. “The murderer must have left it behind him.” “V. V.—341. I can make no sense of that.” The sergeant kept turning it over in his big fingers. “What’s V. V.? Somebody’s initials, maybe.”

You’re supposed to think that V.V. is the initials of a person - the person that killed Birdy Edwards. But it’s not a person - it’s the name of a group: Vermissa Valley Lodge 341 - who are, in fact, trying to kill Birdy Edwards. Likewise, Mary tells you AGRA is the initials of a person - but it’s really the initials of a group who are trying to kill her.

And interestingly, Mary Morstan comes from The Sign of the Four in which there are a group of four bad guys. I think, in BBC, those guys are A, G, R, and A (for example, Jane Allen, Mark Gourd, Sam Rizzo, and Claire Atherman). Remember the other big time we see an acronym - HOUND - and those letters turn out to be people’s initials:

Mary probably knows who the people who want to hurt her, but I don’t think it’s strange at all that she wouldn’t make the connection that they are AGRA. That’s only one letter of their name each. Especially if she thinks they’re in jail or dead.

Back to the punctuation:

(Some of) the people who are after Mary are John’s assassin and Mrs. Hudson’s assassin from TRF. They know Mary via Jim, but they don’t connect the person they know as Mary Morstan to the person they’re looking for. I had been thinking there had to be two more people they’re looking for Mary with, but not according to the punctuation:



Two punctuated, two not. Two left alive, two dead.

And interestingly, the Casebook names John’s Assassin as Gauss. So I’m thinking:



This guy is A:



And this guy is G:



And R and A are already dead. You know who killed them? Mary. No wonder they’re so pissed.

Summary:

1) AGRA are not Mary’s initials.

2) AGRA are the people after Mary who want to hurt her.

3) The flash drive contains false information.



4) Jim made the flash drive and the lies on it.

5) The punctuation is a clue, either about pips or about the people after Mary or both.

