After the less than comfortable conversation with Haytham, Altair goes quiet and thoughtful in the back of Desmond's mind. Desmond lets him do it, doesn't pry into what he's thinking or why, just logs out of the animus and goes quietly back to the floor he's supposed to be on. By the time he's back at his own desk, Altair is gone (returned to his own time, presumably), leaving Desmond alone to deal with whatever come next with Shay.
"Hey, numbskull!"
Desmond slaps on a docile face, and thinks about how badly he'd like to punch Violet in the face as he turns to look at her.
"What."
"Wow," she says. "Grumpy much?" Desmond says nothing, so she scoffs and goes on. "Just wanted to tell you there's a little glitch in the memory sequence you're working with. Not your fault, this time, so that's good for you. And it's really nothing to worry about, barely even worth mentioning. But the next memory is going to be just a little bit farther along in Shay's life."
"How far, exactly?" Desmond asks. He's suspicious of this sudden glitch, the timing is just too convenient. Five minutes ago he was in Shay's future, and now suddenly there's a glitch showing who-knows-what. It would be exactly Desmond's kind of luck if he gets into the memory and sees Connor and Haytham and maybe even himself…
His mind races and he starts thinking of excuses for why he can't get into the animus right now, but Violet surprises him by physically grabbing him and forcing him down and into his seat. "Come on," she says. "I don't have all day, and this is what we pay you for. Get a move on."
Technically, every piece of information Desmond had provided Abstergo when he came in undercover had been false, so his pay was going into an account he will never be stupid enough to actually touch. But there's no use arguing, not when Violet's literally standing right behind him. So Desmond heaves a sigh ("Stop being so dramatic, numbskull") and logs into the animus.
Immediately, he realizes something is wrong. This is not a little glitch, this is the entire world coming apart at the seams. Desmond's brain feels like a television tuned to a bad channel, all hissing static chewing at his brain. He's in Shay's mind, and as that seems like the only solid thing in the world, Desmond clings to him with something like desperation. Nothing is fully loaded, and everything is sort of surreal, half there and half not.
"Desmond!" Shay says, and this is not the same man Desmond had just seen through Haytham's mind. This is Shay from the same point in his life as he had been when Desmond last left the animus, a newly minted templar brought forward in his own timeline thanks to a combination of animus glitch and his connection to Desmond. "What's going on?"
Except that Desmond doesn't know what this is, either, because if it's just a glitch in the animus, Shay shouldn't be aware there's anything wrong (should he?). It looks strange to Desmond because this is a memory he hasn't synced with yet, but this is Shay's own memory. It's probably just the artifact, but still…
"Desmond!"
He shakes himself out of his distraction because Shay sounds like he's struggling to keep himself from panicking. At least Desmond is familiar with the animus- Shay, obviously, is not. So Desmond says "Listen" and Shay does. He quiets, and waits for Desmond to make sense of all this. Later, Desmond will remember this moment as the one when he stops caring if Shay is an assassin or a templar. From this point on, Shay becomes just like the rest of them.
They're all stuck with each other, inseparably bound together in the most personal way possible. And nothing can keep them apart for long- Desmond has risked almost everything to get his ancestors back when the apples were drained. They'd rescued him from the apple when there was no reason to think he was even alive. Together, they'd stumbled their way through learning the apples and time travel. They have given everything to the others, and there's no excuse for doing anything les with Shay, regardless of his loyalties. Besides, he had (he will?) save Connor's life, and that's got to be worth a little bit of trust. This is just (yet another) confusing twist to figure out and deal with, and they will do exactly that.
"Okay," he says. "Here's how it is. I'm using a machine called an animus to see your memories."
"I know," Shay snaps. "We've been over this."
"Well it's…." Desmond flails mentally, struggling to find a way to explain computer glitches. "Broken. Just a little."
"So?"
"So it skipped ahead," Desmond explains. "And because of that artifact from Lisbon-" And Shay doesn't move at all but in his mind he flinches away from Desmond like he's been struck (And Desmond thinks wow this guy needs therapy). "Because of that," he goes on, "I guess it skipped for you instead of just for me."
"Lucky me," Shay says, still obviously upset. "I have to see my own life out of order."
"I thought you make your own luck?"
"…shut up," Shay says, but he sounds more cheerful, weirdly enough. "So what am I doing here?"
"Your guess is as good as mine," Desmond says. "Where is this, anyway?"
"Paris," Shay says with absolute certainty. "I came here once when I was younger. There were these girls-"
"I don't even want to know," Desmond says hastily, before Shay can really get going. He looks around, spots something in the distance, and points it out to Shay. There's not much actually loaded in this memory, so they run after the only thing that seems worth investigating. And in the end, it doesn't take long to get past the out of place memory (although they never exactly figure out how they got to France in the first place). When it's over, Shay's memories pick up smoothly where Desmond had left off at the end of his last animus session, and on the outside it looks like nothing has changed. Only Desmond and Shay recognize the difference, because no one else can tell that now they're really working together, the way Desmond is used to with his ancestors. And it feels great.
Later, when Desmond logs out of the animus for the day, he finds Altair in his head again.
"So about Shay," he says. "I was thinking-"
"I know," Altair says, grudgingly. And there's no more discussion after that. They just accept Shay as he is, and things start to go much more smoothly.
-/-
I've been debating how I should do the incomplete memories for ages and finally I figured I'd just throw words at the page and see what sticks
