Desmond never thought it would happen. From his first moment inside the animus, he knew that his ancestor was nothing but a jackass, and "full synchronization" was nothing more than a fantasy. It surprised him, then, how soon it did happen: when the old man whose name he hadn't bothered to memorize yet was lecturing.
"First, stay your blade-"
"from the blood of an innocent, I know this." snarled Desmond and Altair together. But Altair lashed out against his teacher in pride and anger, and Desmond against his parents, with all the anger and cynicism of a fifteen-year-old boy who had known that no one is innocent. The moment was lost as quickly as it came, and it was Altair alone who received the slap for their impudence. Desmond had already run away.
For an assassination and a half, it had gone on this way, Desmond watching and controlling, the way he had in the video games his parents had let him play occasionally in the compound. It was the Desmond who played video games that decided the madman was a liability and in the way, but it was Desmond-who-was-Altair who felt the still-warm body slip from his hands to the floor. Altair would have said something about being at peace to the man as he choked on his last breath, but Desmond was speechless with sudden and unexpected guilt, and only shut the madman's eyes. He didn't need to look at the bars the animus provided him to know that he had lost synchronization. Altair would have known what to say. Altair wouldn't have killed an innocent, and for the first time Desmond understood the first tenet of the creed. Maybe no one is innocent, but so very few are guilty enough to die.
It bled from small incidents, like the feel of sandstone under his fingertips as he climbed, to larger and larger things, like his tolerant annoyance when the arms master called for his aid again. He'd a mission to be off on, but people had been asking him for demonstrations since he'd graduated first in armed combat. So it was that Altair found himself riding from Jerusalem, spurring his steed on to greater and greater speed. He must stop Robert. He must save the brotherhood. Altair continued on foot past the blockade, cutting down Richard's and Salah Ad-Din's men indiscriminately. He was frightened for himself and frightened for the brotherhood, and he was quite surprised not to die when he saw the arrow shaft spring up in his chest. It was followed by another and another, and Altair didn't get the chance to see which army the archer belonged to or wonder that he didn't feel any pain, before he saw Altair standing in the blue space he thought of as the Animus' loading screen. With a shock Desmond realized that he was a bartender, the year is 2012, he had never climbed a building or killed anyone and had hated blades. He had specialized in pistols, when his parents had given him a choice.
The shock of losing synchronization leads him to watching Altair move and speak, a level of distance he hasn't felt for what seems like months. And it is only through this distance that Desmond realizes – Altair is small. And so fragile. He has always been a solid figure in Desmond's mind, from the moment he appeared cockily disregarding his allies' advice, through each perfect assassination. And only now does Desmond realize that Altair is only one man, small beneath the layers of clothing and weapons and arrogance, and he had no guarantee to success or even survival. Altair is afraid – if he doesn't feel it as his own emotion anymore Desmond can still recognize it in the tight set of Altair's shoulders as he talks to Richard. He came against his survival instincts for the sake of his clan, and to keep the piece of Eden from the hands of the Templars. Can his descendant do any less?
Desmond has been trying to escape from the moment he woke up in the Abstergo facility, but he can sense they are close to the memory Abstergo wants, and knows now he won't get out of the facility before they reach it. What he can do, he thinks, is cause desynchronization; he knows Altair well enough to know what his ancestor would never have done. Desmond will sabotage his work in the animus until Vidic leaves for the night, and then he will find another escape. The towels will do, he thinks. There are pipes in the bathroom, and he's pretty sure he remembers how to tie a noose.
Tonight, Desmond will follow Altair into certain death for the sake of his brothers.
And in the end, it is this very parallelism that destroys him. Desmond tries to remain separate, but there is nothing to do but fight, consumed with fear for his clansmen and himself, and before Altair knows it he is back at Masyaf, feeling deeply the betrayal of his master and regret for killing the brothers in his way, most of whom he's grown up with.
It's not until Altair is lost in confusion and Desmond recognizes a holographic globe that he remembers that Altair and Desmond are separate people. He wails a silent denial, and tries to turn around and stab Malik, jump off the cliff, anything to break the Animus' contact with this memory. But it's too late, the globe has spun once and he knows that's all they need, and the animus is bringing him out of the memory.
- after Abstergo leaves him to rot in a room written over in one of his brother's blood, after Lucy returns splattered with more blood, after they run though aisles of countless versions of the machine that has destroyed and created his life, after he feels someone's trachea collapse under his own hand –
- Afterward, it is the memory of a small figure in white amidst a sea of plate metal armor that gives Desmond the strength to close the man's eyes, whisper a blessing he never really forgot, and jump into the trunk Lucy has opened.