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Animus Island
  • 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. OK, 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 woke up in the Black Room, before taking 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 close to Desmond's position, startling him.

  • Clay: So did I!

Clay laughed.

  • Desmond: Hey!
  • Clay: Look at me now! 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 images 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?

A digital tone could be heard, similar to that of when a telephone was answered. Afterwards, 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...
After DNA Sequence 1
  • William: This Apple... it is a remarkable piece of work. Feel the material... hard as steel but very light.
  • Rebecca: You really want to be fooling with that thing?
  • William: I do. I absolutely do. I have been waiting a long time to get my hands on one of these.
  • Rebecca: Okay, you're making me nervous, Bill.
  • William: Don't be. I don't think I have the right genes to properly wield it.
  • Rebecca: Oh, but Desmond... you think he does?

Desmond was forcibly returned to Animus Island from Ezio's memories.

  • Desmond: What the hell just happened?
  • Clay: You were snooping. Wandering outside the Desmond partition. So once the Animus located you, it pulled you back here. It's just following orders... like a failsafe program. Trying to keep your poor head intact, whether you like it or not.
  • Desmond: And what are you doing here exactly?
  • Clay: Playing. Learning. Waiting. A lot of waiting. I keep the Animus distracted as best I can. For you, so you can explore. Otherwise it might hunt you down like a little virus and ah... delete you.
  • Desmond: Well, my guardian angel.
  • Clay: There's no such thing.

Clay disappeared.

  • Desmond: Yeah I—Thanks.

Another conversation between Rebecca and Shaun could be heard through Animus Island.

  • Rebecca: Shaun, it's me. What's happening?
  • Shaun: Are you at the airport?
  • Rebecca: Yeah, we're chartering a jet. Are you coming?
  • Shaun: Yes. Yeah, I'll be there soon.
  • Rebecca: Good.
  • Shaun: They... they buried her already.
  • Rebecca: I heard.
  • Shaun: In a little cemetery outside Rome. Nice place.
  • Rebecca: God, things got so fucked up so fast.
  • Shaun: Is Desmond still out?
  • Rebecca: Yeah. We're seeing a lot of brain activity, but with the monitoring system shut down, we can't record anything.
  • Shaun: Well, keep me posted, okay? I'll see you soon.
After DNA Sequence 2

Once more, a conversation could be overheard, which featured Rebecca and William Miles.

  • Rebecca: I'm seeing very strange activity in the Animus.
  • William: Oh?
  • Rebecca: The CPU should be fairly idle. But the system monitor is spiking regularly. Sometimes as high as 85 percent.
  • William: Is it serious?
  • Rebecca: I'm not sure. Desmond's signs are stable.
  • William: Well, if there isn't a problem, let's not try to fix anything.
  • Rebecca: Fair enough. God, I need a drink.

Desmond then came across Clay, lamenting on his misfortune.

  • Desmond: 16?
  • Clay: Desmond, think about this... What if... I went with you?
  • Desmond: With me? Where?
  • Clay: It could work. Just for a while. Until I found a way out. Another body maybe. Or... I don't know. I just don't... I don't want to be here anymore.
  • Desmond: That's... that's not going to happen. I'm sorry.
  • Clay: No... I guess I had my chance. And I wasted it.

Clay disappeared.
After a while, a discussion between Rebecca, Shaun and William Miles could be heard.

  • William: Were they close, Desmond and Lucy? I mean... closer than friends?
  • Rebecca: Ah... Well, there was the occasional misty-eyed moment, but—
  • Shaun: She liked him, Bill. That's what she told me.
  • William: Hmm. Interesting.
  • Rebecca: That's it? Just... interesting?
  • William: I spent a lot of time training each of them when they were younger. She was a remarkable woman, and I find this whole situation... quite sad.
  • Shaun: Sad? Are you finally going soft on us, Bill?
After DNA Sequence 6

Some time later, another talk between Shaun and William Miles took place.

  • Shaun: You know something, don't you? You know what's out there.
  • William: I have a hunch, yes.
  • Shaun: Come on, Bill. You never do anything halfway. What do you think we'll find?
  • William: If we're lucky, another prize. If we're very lucky... something that'll end this miserable war.
  • Shaun: You're talking over my head, mate.
  • William: Listen Shaun, I have no idea what we're going to find. But I do know that whatever it is, the Templars can't have it.

After this exchange, Clay inquired about Desmond's life, which at first he was nervous to reply to.

  • Clay: Do you regret anything Desmond?
  • Desmond: Like what?
  • Clay: Running away. Leaving your parents behind. Finding a shit job, and pretending to be productive. What's it like spending your whole life, avoiding hard decisions?
  • Desmond: Come on.
  • Clay: Sure, you're an Assassin, but it wasn't your choice.
  • Desmond: Do you have a point?
  • Clay: I want to know, if you regret anything.
  • Desmond: Sure. I wish I'd been more patient with my parents. I wish I'd listened. And Lucy... maybe things could have been different if I'd—I'm not sure.
  • Clay: Thank you.
  • Desmond: For what?
  • Clay: For making sense.

Once Clay's curiosity was fulfilled, another group conversation with those outside the Animus started.

  • Rebecca: Shaun, you feeling okay?
  • Shaun: Sure, yeah, yeah, I'm fine yeah. We're Assassins, after all aren't we, eh? Why should we be surprised if one of us dies every now and again?
  • Rebecca: Every death is a tragedy. To somebody, somewhere.
  • Shaun: What I want to know is... is Desmond worth all this trouble, you know? What is he... is he the chosen one, is that it? Little Jimmy Special or some bollocks like that?
  • William: I'm afraid not. But what he has is rare. His genes contain high concentrations of First Civilization DNA. Only about one in ten million are so lucky.
  • Rebecca: Ah. The Bleeding Effect. Is that part of it?
  • William: I believe so. I wish I could say we knew about his gift earlier. But it was the Templars who realized this. And they found him first...
After DNA Sequence 8

Following Desmond exploring more of Ezio's memories, the Assassins outside of his coma planned to relocate themselves, and him along with them.

  • Gavin: Bill! Good to see you. Listen, we've got a customs officer waiting to talk to everyone.
  • William: I hope you have something for us.
  • Gavin: Absolutely, passports and papers for everyone.
  • Shaun: Ah brilliant, so I'm... I'm what, a neurosurgeon now, am I?
  • Gavin: You're a medical team from SUNY upstate, just back from Rome with your patient, experimental gene therapy.
  • William: Good work, let's get this over with.
  • Rebecca: Wait look, this is crazy!
  • William: What's wrong?
  • Rebecca: Not sure, but Desmond's brain is lighting up like a string of firecrackers!

Meanwhile, inside the Animus, the machine planned to wipe Animus Island of all its contents, with Clay and Desmond along with it. As the threat of being deleted was finally at hand, it spurred one last conversation between the two.

  • Clay: Here it comes...
  • Desmond: What is that?! What's going on!
  • Clay: This is the end Desmond. Scheduled for deletion!

Clay embraced Desmond tightly, bewildering the Assassin in the process.

  • Desmond: What are you doing?!
  • Clay: What is a man but the sum of his memories? We are the stories we live! The tales we tell ourselves!

Jumping to the conclusion that Clay intended to take both of them to their deaths, Desmond pleaded with him.

  • Desmond: Don't do this!
  • Clay: I'm saving you, idiot! GO!

Clay pushed Desmond towards the Sync Nexus, as he began to be erased by the system deletion. However, it would not stop him from shouting out one final command to Desmond.

  • Clay: GO!
The Sync Nexus

Once Desmond had achieved the necessary synchronization with his ancestors, he found himself communicating with Jupiter, one of the First Civilization, as Juno and Minerva stood at either side of the ancient figure before him.

  • Jupiter: Do you hear me, cipher? Can you see me? Ah. There you are. Good. A strange place, this nexus of time. I am not used to the...calculations. That has always been Minerva's domain. I see you still have many questions. Who were we? What became of us? What do we desire of you? You will have your answers. Only listen and I will tell you how. Both before the end and after, we sought to save the world. We built vaults within which to work, each dedicated to a different method of salvation. They were placed underground to avoid the war which raged above, and also as a precaution, should we fail in our efforts. Each vault's knowledge was transmitted to a single place. It was our duty—mine, Minerva's, and Juno's—to sort and sample all that was collected. We chose those solutions which held the most promise, and devoted ourselves to testing their merits. Six we tried in succession, each more encouraging than the last. But none worked. And then the world ended... The Earth shook for days. The fires burned for weeks. And when the ash had settled, less than ten thousand of your kind still lived... and far fewer of ours. But we carried on, together. To rebuild. To renew. Listen. You must go there. To the place where we labored... labored and lost. Take my words. Pass them from your head into your hands. That is how you will open the way. But be warned: much still remains in flux. And I do not know how things will end—either in my time or yours.
After DNA Sequence 9

Following Jupiter's message and having fully separated himself from his ancestors and their memories, Desmond began to awaken from his comatose state.

  • Rebecca: Wait, look! His vitals are stabilizing... Something's happening... He's... He's moving!
  • William: Desmond, can you hear me? Son?
  • Desmond: I know what we need to do.
Animi Training Program

On the advancement of the Animi Training Program, select Abstergo recruits were allocated to the second stage of the program, and came into contact with Warren Vidic often, as well as some other Templars.
Welcome
Taking place in a dark, dimly lit room, Warren Vidic introduced himself to the prospective Abstergo recruits who had excelled in the program's first stage.

  • Vidic: It is a privilege for each one of you to be invited up here. Everyone in this room has proven themselves as more than mere killers. Your skill acquisition in the Animus thus far has been far superior to that of your colleagues, who, as I speak, continue to struggle down below us. But the test of your true worth has barely begun. You think you know of our Order. Of our founding in 1119, our quest for domination during the Crusades. The vast treasure and the decline at the end of the 12th century. And, finally, our resurgence as Abstergo. You know nothing. It is time to begin your real education. As you continue your training in the Animus, those worthy will be admitted to the secrets of our Order. My assistant will monitor your progress. Once you exit this room there is no turning back. Succeed, and a bright future awaits, fail... and far more than your contract will be terminated.

First Steps
From their previous first meeting, one Abstergo recruit, Juhani Otso Berg, had began to impress the Templar Order, so much so that Vidic offered encouraging words to help motivate him to climb higher.

  • Vidic: You served Abstergo well, and your skills in the Animus continue to impress. I do not use that term lightly. If you continue at this rate, it is a foregone conclusion that you will be the one to enter our inner chambers, and learn our most trusted secrets. Once you cross that threshold, your eyes will be opened, and you will see this world for what it truly is. Don't muck this up. Abstergo is counting on you.

Promises
As usual, Berg had built upon his progress at a quick rate, which impressed Warren Vidic's assistant and called for another meeting with him.

  • Vidic: Moving up through the ranks nicely, I see. Exactly as predicted. My assistant's reports have been glowing, although I find he is a little bit of a panderer. Do not let his flattery fool you. We will only continue to educate you as long as you continue to show promise. Prove yourself, however, and we are prepared to give you far more.

Privileges
With Berg's development bolstered as he invested more effort into the Animi Training Program, his effort began to bear fruit, while Vidic provided a commentary of what differed him from the rest of humanity.

  • Vidic: For the vast majority of humankind, life is an ordeal to be suffered.

Berg chose a designer watch from a box before him, courtesy of Abstergo.

  • Vidic: One painful failure after another, followed, mercifully, by death.

Berg then took a glass of champagne offered to him and entered a private jet.

  • Vidic: Mortgages, car payments, waiting lists, bills.

Berg casually strolled through an airport.

  • Attendant: Right this way, sir.*Vidic: Most are kept far too busy to look at the big picture. But not you. From now on, you will be at the front of every list. Transportation, maids, cooks will all be provided.

From there, he entered a limousine and picked up a bottle of expensive wine.

  • Vidic: Vacation homes, tranquility and privacy will surround you. Your children will attend the best schools, and your parents will be cared for.

Berg pulled up at a remote countryside mansion.

  • Vidic: Any woman, or man, you desire will be yours. For most, life is an unwinnable game.

Berg opened the door and stepped out of the limousine, and Vidic walked out of the mansion's entrance, waiting to greet him.

  • Vidic: The Order of the Knights Templar welcomes you. After all, we engineered it that way.

Inducted
Following Berg's luxurious treatment, Vidic prepared to impart an important message to him, though he was interrupted.

  • Vidic: I hope you are enjoying the new comforts we have granted you. Of course, you know there is no backing out now. We have plans for you. An important part of this company's future. Truth is—
  • Intercom: Dr. Vidic. You are wanted in the processing plant.
  • Vidic: Well... I suppose the truth will have to wait.

Clearance
Determined not to disappoint, Berg had progressed even more since Vidic's last visit, prompting him to tempt at allowing Berg deeper into the Templar Order.

  • Vidic: I see you have been busy while I was gone. Continue to increase in skill, and you may be invited to visit our inner offices. Be respectful, far more than your job is on the line. I have put in a request to have your security clearance raised, allowing us to share sensitive information with you. Something to look forward to... If you make it, of course.

Active Agent
Soon enough, with the growth of skill that Berg had shown, Vidic made mention of his first mission, as well as his final briefing, as he encroached upon the completion of the Animi Training Program.

  • Vidic: Your training is almost complete. Allow me a rare moment of emotion, I feel proud of my accomplishment. Soon, you will become an active agent. Others have been sent to gather the intelligence required for your first mission as we speak. Conclude your training and the final briefing will occur upstairs. May the Father of Understanding guide you.

One of Them
Rather slowly, Berg entered the secret chamber located within the corporation after using a fingerprint scanner, making sure to pay attention to all of he saw. Hearing a voice, he sat down as he was asked, before Laetitia England introduced herself to him.

  • Laetitia: Very few people ever see this room. It was first decorated in 1937, when we first founded the company. Laetitia England. Warren has told me so much about you. Quite impressive, reaching such a privileged position. The remnants of the Assassin Order are scattered across the globe. The time has come to end this fight. And you will be on the front lines. It comes down to trust. We must be certain that ours is well placed.

A gruff sounding voice suddenly stated an order.

  • Daniel: Don't move.

Panicking slightly, Berg attempted to get up, but was held still by an arm around the throat, the hand holding an injection gun.

  • Laetitia: Daniel, I give the orders.
  • Daniel: Fine.
  • Laetitia: Thank you. Now, go on.

Proceeding onward, Daniel implanted Berg with a microchip from the injection gun.

  • Daniel: There.
  • Laetitia: From this day forward we monitor your every move. Welcome to the fold Master Templar.

Target Acquired
Newly appointed as a Master Templar, Berg sat observing the figures before him during his briefing, who had an announcement to make regarding the Assassins.

  • Vidic: You have all been brought here because our intelligence gathering has progressed rapidly in the last week.
  • Daniel: What have they found?
  • Vidic: Be patient Daniel. I have an announcement to make. We now know where the Assassin leader, William M., is located.
  • Laetitia: Brilliant work. We need to send a retrieval team.

The two Templars then turned to Berg, staring straight at him.

  • Vidic: Well, what are you waiting for? Go get him.
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