Alternate Universe Details:
This AU is more or less a role swap and history change up. In this universe, Clay is the one who has to save the world in 2012 from the solar flare - not Desmond. This is about to get tl;dr so beware! This is also based off Revelations, due to the current canon points in Mandalus.
Clay's backstory remains namely the same. His father drills it into his head that he has to be an engineer, like the rest of the family, and he suffers from depression, low self-esteem and low self-worth. He is still a descendant of Ezio Auditore, but in this universe he is the descendant of Ezio and Sofia's son Marcello, allowing him to access more of the ancestral memories in the Animus. While Minerva and Jupiter worked to have Desmond be the one to save the world, Juno chose Clay and began to manipulate the family line at certain points that would lead Clay to the Grand Temple. After the death of Desmond Miles, Clay became Subject 17 and the target of Warren Vidic's
Project Siren. He goes on to relive Ezio Auditore's life with Shaun Hastings, Rebecca Crane, and Lucy to not only train him as an assassin, but to find more of the Pieces of Eden. Clay discovers the message from Minerva left for Desmond, then causing the team to go further into Ezio's memories to try and discover what it is that Desmond was meant to do. They discover the location of the Grand Temple (The Da Vinci Disappearance) and then the location of Ezio's Apple, in hopes of being able to do whatever it was that Minerva wanted Desmond to do. Clay encounters Juno at the Colosseum, then is controlled by the Apple to kill Lucy. Clay falls into coma due to the shock of her death, what he learned from the Apple, and the Bleeding Effect. He finds himself in the Animus Black Room to piece his mind back together. Despite the message from Ezio ultimately being for Desmond, at the completion of the Synch Nexus, Clay encounters Juno who tells him to go to the Grand Temple and open the door so that he can save the world and do what Desmond failed to do.
Desmond's backstory remains mostly in tact. He's descended from Flavia, Ezio's eldest daughter as he is in the canon timeline. Instead of running away at sixteen, Desmond elects to be cut off from the Order in hopes of being able to infiltrate the Templars to learn what they are planning. Eight years later, at the age of 24, Desmond reunites with his father, Shaun Hastings and Rebecca Crane to plan their next move. Desmond, instead of Clay, then offers himself as a test subject to Abstergo Industries and becomes Subject 16. He spends days in the Animus at a time and eventually comes into contact with Minerva through the Bleeding Effect in Ezio's memories. He then later comes into contact with Juno, after learning what Minerva later reveals in Assassin's Creed III, agrees to aid the plot of Juno. Despite his decaying mental status, Desmond begins to try and leave clues for Clay to follow to finish what he can't. Desmond was informed by his father that when things got bad, the mole Lucy Stillman would help free him. Lucy and Desmond grew close, with Desmond falling in love with her, but learns from Juno that Lucy is truly a Templar. Knowing there's no way out, Desmond begins to program the Animus to reconstruct his memories to aid Clay, as he is aware that Abstergo has found him. His first attempt of leaving Abstergo was through force, which led Desmond to cutting his arms to write cryptic messages on the walls. Given Lucy's attachment to Desmond, the Templars patched him up enough to be placed in the Animus again, making it so Desmond survives the suicide attempt.
The change in the whole story is that Clay witnesses Desmond (Subject 16) die. The day that Clay is brought to Abstergo, Desmond attempts again to escape. He manages to get down to the lower levels of Abstergo and grabs Clay, trying to desperately pass along what knowledge he has. Except Desmond's mind is far too gone and he speaks in broken Italian and Arabic. Desmond then fights off the guards and grows increasingly violent, causing the security to shoot him on site. Clay is taken up to the room that Desmond once was in, and Desmond is pronounced dead when the ambulances arrive. Desmond's AI then goes on to help Clay learn what he needs to know in order to save the world.
BASICALLY: Desmond was the way Minerva and Jupiter wanted to save the world, Clay was the way Juno wanted to. Desmond decides to support Clay as he can't go on further and becomes the one to leave clues in the Animus and to later guide Clay through the Synch Nexus of Revelations. Desmond's AI is also destroyed in Revelations to save Clay from deletion. It also shifts the dynamic of the supporter to Desmond to help Clay overcome his own self doubts to put the others and the Creed first. Desmond is also the assassin, while Clay is the recruit with Animus training. Desmond is the one who is ultimately unhinged and not all there, while Clay is the one dealing with the guilt that Desmond died for Clay.
BONUS FUN:
Conversations that were written up to reflect the differences in this AU for ACR!
[ ANIMUS BLACK ROOM. Clay begins to wander the Island. Based on
THIS. ]
Desmond Miles: So, you're going to just walk past me? That's pretty rude, you know.
Clay Kaczmarek: ...Sixteen?
Desmond Miles: Actually, it's Desmond. Welcome to Animus Limbo. Do not pass go, do not collect 200$. Not until you get your head on straight.
Clay Kaczmarek: YOU'RE DEAD. I SAW YOU DIE.
Desmond Miles: And you're a vegetable, don't judge. Come on. There's a lot of work for you to do and not a lot of time left... by the way. Lucy. Did you...?
Clay Kaczmarek: She's...dead. You said someone was lying.... It was her.
Desmond Miles: Good. Then we don't need to worry about that. Glad something I said made sense. You know, since I'm basically crazy.
Clay Kaczmarek: There was a lot of crazy you were spouting. Did you say something about whores, or did I hear that wrong?
Desmond Miles: You know Italian? huh.
Clay Kaczmarek: Now, I do.
[ ANIMUS BLACK ROOM. Desmond confronts Clay through progression of Synch Nexus. Based on
THIS. ]
Desmond Miles: You ARE an assassin if you chose to. Make the choice. If not, then maybe I should step into your body and do it for you.
Clay Kaczmarek: You can do that?
Desmond Miles: Probably. You sure of hell are too much of a pussy to make the choice. Why the hell did I die for you if you're gonna sit here and feel sorry for yourself? How about YOU stay in the fucking Animus and I do it for you? Since you needed Daddy to tell you how to do everything anyways.
Clay Kaczmarek: Fuck you, man. I didn't ask for any of this shit. I grew up hearing that I was supposed to be one goddamn thing. Then suddenly I'm the savior of the world? That's a lot of shit to put on a guy.
Desmond Miles: And you think being cut off from my FAMILY for eight years, being pulled back, then suffering inside the Animus for an entire year waiting for your sorry ass to show up isn't? I lived more lives than I can count for more hours than I even know. And then, on top of it? The woman I loved betrayed me a long time ago. Make your choice. You either do this, or I'm doing it for you, because it has to be done.
Clay Kaczmarek: You don't even fucking know me. Why would you do this? Leave those messages. Make this...version of you. Why would you do it if you have zero fucking faith in me?
Desmond Miles: I do know you. What the hell do you think I've been doing in here while you've been running off as Ezio? Your memories are stored in here just like mine are. Like all of ours. I know more about you than you even remember. And, maybe I do have faith in you. You just don't want to see it because it's easier being a fucking coward than actually trying.
Clay Kaczmarek: What's the point in trying if I'm just going to fail. I learned from a very young age that whatever I do isn't good enough. Not for him, not for anybody.
Desmond Miles: Then fuck him. You know who matters? Ezio. Look at what that guy did so you could stand right here and talk this shit. He's the one you're letting down. Not your dad.
[ Comment hits Clay right in the heartstrings. ]
Desmond Miles: So make the choice. You either do it for a guy who lost everything so you could stand here, or you let yourself be trapped by what an asshole said. Make it soon or you might as well just let everyone die anyways.
[ Desmond disappears in a flash of light. Clay returns to the Synch Nexus. ]