By age 16, Desmond became tired of living in hiding and aspired to pursue his own dreams. Using the minimal training of Assassin skills he had obtained from his father, William Miles, Desmond fled from the Assassin compound he had grown up in and managed to travel from South Dakota to New York City, where he found employment as a bartender in the Bad Weather nightclub.
In September 2012, Desmond was kidnapped and incarcerated by Abstergo Industries, a Templar organization, and forced into a machine called the Animus to relive the genetic memories of his ancestor, Altaïr Ibn-La'Ahad. It was Abstergo's aim to acquire a map that detailed many "Pieces of Eden" spread across the Earth, which Desmond was reluctantly successful in doing. Following this, he managed to escape Abstergo with the help of Lucy Stillman, an undercover Assassin, and joined an Assassin cell in Italy, which consisted of herself, Shaun Hastings and Rebecca Crane. Utilizing an upgraded Animus of Rebecca's construction, Desmond relived the memories of Ezio Auditore da Firenze, in order to improve upon his newly obtained skills.
Eventually, with the knowledge gained from Ezio's memories, Desmond and his fellow Assassins obtained the location of Ezio's Apple of Eden, which was located underneath the Colosseum. Though successful in obtaining the artifact, Desmond's body was taken over by Juno, a member of the First Civilization, and was made to stab Lucy after Juno revealed her to be a traitor. As a result of the shock, Desmond fell into a coma, and was placed in the Black Room, the safe mode of the Animus, in an attempt to stabilize his condition. With help from the virtual construct of Clay Kaczmarek, "Subject 16" of Abstergo's Animus Project, Desmond was able to regain consciousness, and found himself located in the state of New York once more, this time with Rebecca, Shaun, and his father, William.
While in the Grand Temple, Desmond relived the memories of Haytham Kenway and Ratonhnhaké:ton to find the key to the sanctum containing the device needed to prevent a devastating solar wind. He also undertook field missions to retrieve power sources for the Temple, coming into conflict with Daniel Cross. After his father was captured, Desmond rescued him from Abstergo's Roman facility, and assassinated Cross and Warren Vidic in the process.
After finding the key, Desmond opened the sanctum, but discovered he had been misled. It was made known that the device would save the world, but also unleash Juno, who had been imprisoned because of her hatred for humanity; using the device would also claim Desmond's life. Regardless, Desmond chose to sacrifice himself for humanity's survival, while expressing faith that his fellow Assassins would find a way to stop the new threat.
Desmond was born in an Assassin hideout near to the Black Hills, west of Rapid City, in the United States. Known as "the Farm", the hideout was an off-the-grid compound with a population of around thirty people, all leading a nomadic lifestyle.
Desmond trained along with the other children of the Farm under the supervision of William Miles, his father, which proved to be extremely intense, often scaring him. He was also instructed to always be wary of their enemies, though as he grew older, Desmond became bored by the war stories of the Assassins and Templars, and underestimated Abstergo's influence over the world as a result. Finally concluding his parents to be little more than conspiracy freaks, he decided to leave the compound.
On his sixteenth birthday, Desmond ran away from the Farm. His training proved to be useful, as he was able to outrun and avoid the Assassins who had pursued after him. Following this, Desmond traveled through "the badlands" and hitch-hiked for some time, until he eventually came across a person who advised him to go to New York City, prompting him to leave for the metropolis and blend into the crowds.
Desmond eventually gained employment as a bartender at Bad Weather, most likely due to his looks. While he worked there, his specialty drink was the "Shirley Templar", a Shirley Temple cocktail with gin. Wanting to avoid the Assassins, Desmond never used his real name, and made sure to only use cash to purchase items. Over time, he tried to start a new life, but would sometimes begin to miss his family and old friends.
Unfortunately for him, Desmond was eventually found by Abstergo, after being traced through a fingerprint which was needed for his motorcycle license. Subsequently, he was kidnapped by the Templars, who brought him to an Abstergo laboratory in Italy. The company then went about erasing all evidence of his abduction.
Captured by AbstergoEdit
On 1 September 2012, Desmond was captured by Abstergo agents. The next day, after awakening at an Abstergo facility in Italy, he was held captive for use as a test subject in the Animus, a device that could read the memories of people's ancestors through the "genetic memory" passed down through their descendants' DNA.
At first, Warren Vidic attempted to pry the information he wanted from Desmond's mind, who was out cold, but he was met with failure. When Desmond came to, he angrily claimed to be nothing more than a bartender, but Warren revealed that Abstergo knew of his history as an Assassin, forcing Desmond to finally admit his past life.
Warren and his assistant, Lucy Stillman, told Desmond that they were trying to access a certain memory of his ancestor, but Desmond's subconscious was resisting their efforts. Warren warned Desmond that if he refused to co-operate with their efforts, they would induce him into a coma, continue their work, and leave him to die when they had finished. Without much of a choice, Desmond agreed to help them.
From that point on, Desmond was made to explore through the genetic memories of Altaïr Ibn-La'Ahad – a Syrian man who was a member of the Assassin Order during the High Middle Ages. For several days, Desmond did so under the Templar's watchful eye, but during the nights, he was anonymously given a code that allowed him to open the door to the bedroom provided for him, which granted him the ability to explore the laboratory that he was being held in. As he was presented with the opportunity, Desmond used it to access the Animus' computer, and, after he had stolen Warren's access pen, gain access to Warren's personal computer as well.
Through reading private emails, Desmond learned much about Abstergo, as well as the Animus subject that had preceded him, Subject 16, who was noted to have suffered from the "Bleeding Effect", a drastic symptom induced due to prolonged exposure to the Animus. Eventually, on Lucy's prompting, the Assassins attempted to liberate him, with the gunfire of their assault being heard through an intercom device.
After the rescue attempt failed, Warren boasted that those Assassins were, in fact, the last of the group Desmond had escaped from, and that their desert hideout had been previously destroyed. When Warren left, however, Lucy reassured Desmond that that compound had been found deserted and that his parents had "probably escaped". During this discussion, Lucy revealed herself to be an undercover member of the Assassins.
Subsequently, Desmond eventually achieved Warren's goal and discovered the locations of numerous Pieces of Eden. Following this, three executives of Abstergo Industries ordered for Desmond's execution, but his life was saved by Lucy's intervention, as she asked them to keep Desmond alive in order to re-access his memories if necessary.
After the executives left, Desmond realized that he was able to use "Eagle Vision", an ability that he shared with Altaïr, which he had picked up through the Bleeding Effect. Using it for the first time, he perceived a strong interpretation of Warren and Lucy's true allegiances, as well as countless scrawled messages and puzzles on the walls and floor of the main laboratory and his own quarters.