Editing Desmond Miles (section)

=== Escape to the Hideout===
After Desmond spent some time alone in the laboratory, Lucy suddenly returned, covered in blood and demanding that Desmond was to get into the Animus before Abstergo discovered what she had done. Desmond, rather confused, agreed to her request and managed to synchronize himself with the closest genetic match between him and Subject 16, which was recorded on the Animus' memory core. Inside the Animus, Desmond experienced the birth of another of his ancestors, Ezio Auditore da Firenze, before he was pulled out abruptly, so that the two could both make their escape.

The pair were quickly spotted by Abstergo's security, though Lucy was able to react fast enough to lock a door and keep the guards from reaching them. Unfortunately, they were forced into an engagement with two more security personnel, who Lucy promptly dealt with, astonishing Desmond and allowing them to continue undetected. The two soon entered an elevator, which led down to a large open room filled with office blocks, that housed a large number of Animi.

As Desmond followed Lucy through the maze-like walkways between the blocks, in order to avoid the guard patrols, they eventually reached the back of the room. Lucy attempted to enter a code into the locked door of another elevator, but it was rejected, prompting Desmond to instinctively call upon his recently acquired Eagle Vision. Seeing the buttons necessary for the code, Desmond successfully unlocked the door on his third try. However, once they had both reached the car park underneath the building, the two were halted by more of Abstergo's guards, but were able to defeat them and escape.

Arriving at one of the Assassins' hideouts, Desmond was introduced to two more Assassins – Shaun Hastings and Rebecca Crane – who had previously worked with Lucy. Lucy told Desmond that they wanted him to be trained as an Assassin, which could be achieved in a matter of days, thanks to the Bleeding Effect. Doing so required him to learn through the ancestor that he had matched up with through Subject 16, being Ezio Auditore, and Desmond agreed to help almost immediately, which surprised Lucy. After this, he was quickly plugged into the Animus 2.0, where he began to relive Ezio's memories.

After learning the skills of an Assassin through Ezio's lifetime and the Animus, Desmond was retracted from the machine, partly to test his retention of the techniques he had learned, but also to prevent the mental degradation that Subject 16 had suffered from being placed in the Animus for an extended period of time.

Instructing him with initiating security protocols around the hideout, Lucy left it to Desmond to figure out how to reach them through the use of his Eagle Vision and newfound freerunning skills. Just as he began, however, he started suffering vivid hallucinations of the Third Crusade era. At first, the visions were short, and were nothing to worry about, but after completing the task, Desmond was incapacitated as the visions became more real.

Taken back to medieval Acre by the Bleeding Effect, Desmond once again followed the memories of Altaïr, though this time, without using the Animus. Through the vision, he discovered that Altaïr and Maria Thorpe had conceived a child, Sef, who was to be Desmond's direct ancestor after Altaïr.

The next day, Desmond had recovered from the experiences and returned to the Animus, though he neglected to tell his Assassin teammates about what had happened. From there, he continued to watch the genetic memories of Ezio Auditore, despite at one time being thrown out by "corrupted memory sequences".

Eventually, the team learned that Ezio's nemesis, Rodrigo Borgia, had become Pope Alexander VI in 1492, in order to gain access to both another Piece of Eden, the Papal Staff, and the Vault underneath the Vatican. As Ezio entered this Vault, he was confronted by the hologram of a "goddess", who called herself Minerva.

Minerva warned the Assassins of the end of the world, recounting the story of the war between "The Ones Who Came Before" and their human subjects. The Assassins were shocked when Minerva addressed Desmond by name, confusing even Ezio, and revealed that she was in fact talking to Desmond ''through'' Ezio. Mere moments after, Desmond was quickly pulled out of the Animus, and upon seeing the three rushing to collect their belongings, he realized that the Templars had found their location.

As he climbed out of the Animus, Lucy tossed Desmond a Hidden Blade with the Assassin insignia on the bracer, and asked for his assistance in covering their escape. Making their way into the warehouse, they were confronted by Vidic and several Abstergo security guards, all of whom were intent on reclaiming Desmond.

Together, the two eliminated all of the Templars that assaulted them, with Desmond – now fully synchronized with Ezio and possessing all of his abilities – masterfully using his Hidden Blade to kill many of the guards himself. With his entourage defeated, Warren was left to confront Desmond on his own, though he opted instead to retreat, before promising that their victory was only temporary.

The four Assassins then fled north, with Desmond being hooked up to the Animus inside the van so that he could continue to search through his memories for anything useful. Meanwhile, the other Assassins began to discuss the nature of Minerva and her speech.