- Rebecca: We can keep him like this for a few days, maybe a week.
- William: Call ahead, tell them we're on our way.
- Rebecca: As soon as we're clear.
Rebecca's voic faded as Clay Kaczmarek's digital consciousness spoke from within the Animus while Desmond's comatose mind replayed a montage of his memories, starting with waking from using Abstergo Industries' Animus 1.28.
- Clay: Desmond Miles. Your life has changed so much in so little time.
The memory changed to Lucy opening the back of a moving truck at the Villa Auditore so Desmond could exit.
- Clay: Two months ago, you were pouring shots for bankers and celebrities... But now look at you.
The memory changed to Desmond catching Ezio's Hidden Blade bracer after Lucy tossed it to him.
- Clay: You're an Assassin. One of us.
The memory changed to Desmond, Shaun, Lucy, and Rebecca as they descended into the Colosseum Vault and opened its main door.
- Clay: One of the good guys, isn't that nice? Men and women dedicated to protecting and preserving human life and liberty.
The scene changed to Warren Vidic standing on suspended scaffolding delivering a speach over the Animi Training Program room before morphing to Warren's raid on the Rome hideout.
- Clay: Not like those Templars...cold and calculating autocrats, drunk on power, obsessed with order, all that... we're doing our best to stop them. Yeah, doing our best.
A clip of Clay's mad laughter played as his voice was slightly digitally distorted towards the end. The scene changed to a tracking shot over the Animus 1.28 and a zoom on its physical interface and digital HUD, before forming a construct of Altaïr Ibn-La'Ahad in the Memory Coridor which resolved into a rooftop view of Acre.
- Clay: But you remember all this, right? You remember the Animus, the machine we use to unravel genetic memories and relive the lives of our ancestors? First you were Altaïr, a stoic twelfth-century Assassin from the Holy Land.
The scene changed to an adult Ezio in the Memory Corridor, flickered to his street fight as a young man with Vieri de' Pazzi on the Ponte Vecchio,[2] then flickered again to an adult Ezio charging at Cesare Borgia during the siege of Viana in 1507.[14] Through all this, Animus code kept glitching code lines in, distorting the scenes.
- Clay: Then, you were Ezio Auditore, a wealthy Italian with charisma and a talent for revenge.
The scene changed to Desmond seeing a "ghost" of Ezio in the Villa Auditore's Santuary through the Bleeding Effect.
- Clay: So, what do you three have in common?
As if prompted, Desmond's mind replayed his memory of touching the Apple of Eden in the Colosseum Vault.
- Clay: That's right. The Apple of Eden.
A rapid series of visions passed, starting with Ezio using the Apple to manipulate a Brute into striking a Papal Guard, Ezio collapsing after using the Apple on a group of Borgia guards, and finally to Ezio meeting Minerva. All the while, another clip of Clay's mad laughter played in the background.
- Clay: That strange artifact left behind by... those people. The ones who came before. You know the Apple's power. You felt it for yourself.
Prompted again, Desmond's mind replayed the events in the Colosseum Vault as he stabbed Lucy and then fell into a coma.
- Clay: Oh, it's been fun, hasn't it, Desmond? But that's about to change.
A "ghost" of an adult Ezio appeared before Altaïr in Acre, then Altaïr's "ghost" took the place of one of Ezio's Apple illusions in his fight against Rodrigo in 1499.[7] This "resolved" to both Altaïr and Ezio walking along the Leap of Faith platforms in Masyaf, all as the Animus began to glitch even more code lines into the simulations and Clay's laughter replayed.
- Clay: Your mind is fragmenting, falling to pieces... and if you don't find a way to wake up, you may lose youreslf. Forever.
Overwhelmed by glitches, the Animus cut to black and restarted.
- Rebecca: Okay, I shut down the Animus Monitoring System to free up a lot of memory, but even like this, it's still risky.
- William: Desmond will be fine. The partition worked, the Animus is stable, and his signs are good.
- Rebecca: For now. But this was built to recreate memories, not simulate entire cognitive processes.
- William: The Animus will do its part, and Desmond will do the rest.
Desmond's consciousness woke in the Animus.
- Desmond: What's happening? I... I can't move. I can't— No!
Desmond washed ashore on an island in the Black Room and took some steps forward to adjust to his surroundings. Meanwhile, the digital construct of Clay Kaczmarek initialized nearby.
- Clay: Just walked right past me.
- Desmond: 16?
- Clay: Aw, they didn't tell you my name?
- Desmond: Oh God damn it, I'm still in the Animus?!
- Clay: Quite a shock you've suffered out there.
- Desmond: Rebecca! Get me out of here.
- Clay: They can't help you Desmond. You're a broken man. Your mind, it's... broken.
- Desmond: Broken? I feel fine.
Clay suddenly relocated himself right in Desmond's face, startling him and making him fall on his back.
Clay laughed.
- Desmond: Hey!
- Clay: Look at me now!
Clay extended a hand down to Desmond.
- Clay: Let's talk, buddy. Walk with me.
- Desmond: What is this place?
- Clay: It's nice isn't it? We're in the guts of the Animus, the original test program. No memories here, just basic physics, weather simulations. Hello world! You're lucky someone up there had the sense to plug you in here. Saved your life.
- Desmond: Saved it from what?
- Clay: Right now you should be sitting in a hospital ward, drooling and chewing on your tongue! For now, the Animus is keeping you intact, keeping all your ancestors from collapsing into one big mess. But if you can't find a synch-nexus, all those personalities will smash together. And that won't be pretty.
- Desmond: A synch nexus?
- Clay: I'm getting there, hold on.
Clay pointed to the Synch Nexus.
- Clay: There, that thing, is your way out.
- Desmond: You're screwing with me.
- Clay: Here's the problem, your brain is hash—too many ghosts in your head, too many voices. So, how do you fix that? You claw your way back into the stored data, you find unfinished memories, and you crack them open. Finish what you started—until your ancestor has nothing left to show you. THAT is a sync nexus. Find it, and the Animus can separate Desmond from Ezio and Altaïr, and send you home. Back to your body.
- Desmond: How do you know all this?
- Clay: Because it happened to me. But my body, it's worm food now. So I'm stuck here. A word of warning. When you step through there, everything changes. Nothing feels... normal. But you are still in control and it's up to you to find your way out.
- Desmond: Right.
- Clay: If you hurry, you might make it back in time for Lucy's funeral.
- Desmond: What?
- Clay: Oh. I thought you knew.
Desmond collapsed to the ground, as memories from the Coloseum Vault flashed through his mind.
- Desmond: Lucy... Oh God... I'm so sorry. It wasn't me, it wasn't me, it was that voice! Juno! She took hold of me, she made me... what am I doing? What have I done?
Outside the Animus, a digital tone from an answered telephone was heard and a conversation between Rebecca, Shaun, and William Miles began.
- Rebecca: It's Shaun. Shaun, what's going on?
- William: Let me talk to him.
- Rebecca: Did you... hold on, I'm putting you on speaker.
- William: Shaun, it's William. Is everything taken care of?
- Shaun: Oh, well, hello to you too. For Christ's sakes, man, have some class!
- William: All right, calm down.
- Shaun: Oh, that's rich, yeah. Lucy's dead and you want me to act like it's Easter Sunday, do you?! How's Desmond anyway, kipping in?
- William: That's enough, Shaun!
- Shaun: What if he's a Templar, Bill? Eh? What if he's been programmed?! It's happened before!
- William: No. Not Desmond.
- Shaun: Right. You would say that.
- William: Shaun...
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