Something unexpected happens when Altair uses the apple to go back a year. The plan is to sabotage the animus in the past, before Desmond ever climbs into it. With any luck, the sabotage will keep Abstergo from making records of the sessions, without completely destroying the machine. They want to avoid that, because if Desmond doesn't use the animus, Altair never gets inside his head, and can't go back in time to change anything... basically, it's a paradox, and Altair has no idea how to handle something like that.
The plan is simple, an in and out trip. Altair even knows exactly how to do it- all that time hanging around the temple while Desmond was in Connor's memories, listening in on conversations and watching the assassins at work is paying off in unexpected ways. He doesn't even have to access the computer, just break a loose piece off the animus itself.
He uses the apple to travel to the specific moment he needs to be in. Too soon, and someone's likely to notice and fix the animus. Too late, and they'll still be able to capture some footage. He chooses the morning of the day Desmond is first taken to Abstergo.
The room with the animus is a lot brighter than Altair remembers it from his brief visit almost a year ago. It's not a prison yet, just a room with unusual furniture. The smell of cleaning products lies over everything, and Altair can't help but make a face as he steps toward the animus. Even under the overbearing stench, he can make out the tang of blood. Or maybe that's in his mind, because he knows what's happened in this room.
He's spent a lot of time over the last ten months understanding Abstergo's security, so he feels fairly confident in assuming they won't bother with security recordings on an empty room. External cameras- yes. Cameras in areas with employee traffic- also yes. When Desmond is brought in and set up in the animus, they'll turn the cameras on for him, too.
Right now, though, the cameras are off, and the animus lies unprotected, almost like it's waiting for him. As he draws close, he can hear the animus humming softly to itself, and he can't resist stopping to look at it.
This animus is not a nice looking machine. It's big and ugly, one long slab of metal that looks like it must be incredibly uncomfortable to lie on for any length of time. The humming grows louder, and Altair realizes that it's not really a friendly hum. It's hungry, and maybe a little angry. Or maybe he's just reading too much into what is basically a collection of computers and machinery. Anyway, it's this specific animus that first introduced him to Desmond and started... everything. However much he dislikes it, Altair has to admit that it's sort of a big deal to see it again.
There are footsteps in the hall outside, close and coming closer. Altair crouches down and there, at the base of the animus, and there's the piece he needs, exactly where he expects it to be. External storage- without it, the video from the animus can still be displayed in real time, but not stored and referred to later. He pulls it out and then, with a confidence that comes from months of practice, uses the apple to disappear with it, back to 2013.
As he leaves, he glances toward the door, half curious who the footsteps belong to. He catches a glimpse of three heavily muscled men carrying an unconscious person between them. He knows its Desmond without even looking- after all, who else would they be bringing in on this particular day?
For just a second, he hesitates. He could step in right now, and prevent everything that's about to happen. It wouldn't even be hard. The guards aren't expecting a fight, and the way they carry themselves tell Altair that they wouldn't put up much of a struggle even if they were ready.
But he takes just a second too long to make up his mind, and abruptly finds himself back in the future, on the other side of the world from that particular Abstergo building, still holding the animus piece he went back to get.
A chill, brisk wind picks up abruptly, and Altair pulls the hood up on his jacket and thrusts his hands into his pocket. He's in an alleyway, three blocks from the apartment that's been their safe house for the past few months. It's dirty, so covered in trash and dead leaves that he can barely see the concrete ground under his feet. It matches his mood.
Altair tosses the animus part onto a pile of trash that's been collecting against a building for weeks, and hurries out to the main street. His mind, though, is still in the past, replaying over and over his last few seconds at Abstergo. This isn't the first time he's thought about changing the past. Saving the people he couldn't save without advanced knowledge. He could make peoples' lives better.
But he's never done it, because he knows that once he starts, he'll never stop. Maybe once, that wouldn't have stopped him. Before Desmond, before the apple, he wouldn't have given it a second thought. He's seen a lot since then. He's seen people throughout history make the same mistakes over and over. It all comes down to power. If he was to use the apple to rewrite history, he knows that he'll make those same mistakes. Only he's playing with time, and the consequences would be unimaginably worse.
And besides, rewriting history is something a templar would do. It would be about ordering the world the way he wants it, about taking away free will and exchanging it with his will.
That's just not something he's willing to do.