Editing Desmond Miles (section)

===Exploring the Black Room===

:''"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. That won't be pretty."''
: ―Clay informing Desmond about his mental state.

Due to the intense mental strain, the exposure to the Apple, and the incident with Lucy which caused Desmond to fall into a coma, William Miles – Desmond's father and the ''de facto'' leader of the Assassin Order – ordered Rebecca to place Desmond into the Animus and shut down all of its non-essential functions, stabilizing his condition. As such, this led to Desmond entering the Black Room, a safe mode built into the Animus' core programming.

Upon first awakening on the Animus Island, Desmond was met with a virtual construct of Clay Kaczmarek, Subject 16 of Abstergo's Animus Project. Clay explained that Desmond needed to continue reliving his ancestors' memories until they had nothing left to show him—eventually reaching what Clay called a "Synch Nexus". Once Desmond had located it, the Animus would be able to separate his consciousness from Altaïr and Ezio, and he would be able to wake up.

Clay then coldly remarked that if he hurried, Desmond could make it in time for Lucy's funeral, which bombarded Desmond with flashbacks of the events that transpired in the Colosseum Vault. Desmond felt deep regret for his own actions, but he proceeded to relive the memories of Ezio Auditore, so that he could return to a conscious state.

After completing the first sequence of Ezio's memories, Desmond overheard a conversation between his father and Rebecca. During it, William was examining the Apple, which made Rebecca nervous. However, William reassured her that he did not believe he had the proper genes necessary to use the Apple, with Rebecca following the conversation by guessing that Desmond did.

Desmond was then pulled out of the memory corridor and back to Animus Island, where Clay explained that the Animus had detected him leaving his assigned partition, and had pulled him back to the island, acting as a failsafe program to try to keep his mind intact. Clay also told Desmond that he would keep the Animus distracted, in order to stop the machine from thinking that Desmond was a virus and deleting him.

Whenever he collected enough data fragments scattered across Constantinople, Desmond could enter the core of the Animus and reflect on his own memories—the Farm where he grew up, training as an Assassin, his escape from the Farm, life in New York City, and his eventual capture by Abstergo.

He recalled his relationship with his parents and regretted not listening to them, as well as coming to terms with his role as an Assassin, noting that his easiest days were long gone but that he did not want them anymore.

Between certain sequences, Desmond was pulled out of Ezio's memories, and conversed with Clay upon his return to the Animus Island. The first time they talked with each other, Clay asked Desmond if it was possible that he could go with him once he exited the Animus, and attempt to find another body which he could occupy. However, Desmond hesitantly refused, and Clay remarked that he understood the reason why and lamented on his situation.

Later on, Clay asked Desmond if he regretted anything he had done in his lifetime, like leaving his parents and ignoring his role as an Assassin for so long. In response, Desmond admitted that he wished he had been more patient with his mother and father, as well as confirming to himself that things between him Lucy could have gone differently. Afterwards, Clay thanked him for "making sense".

Being pulled out a third time, Desmond was confronted with the sight of the island disintegrating around him. Clay proclaimed cynically that the Animus had scheduled them for deletion, grabbing onto Desmond as the virtual ground beneath their feet began to fracture.

Desmond was bewildered at both the suddenness of it and whether Clay intended to have both of them die together. He was proven wrong with this doubt, when Clay sacrificed himself, pushing Desmond back through the portal to allow him to relive Ezio's final memories.