William Miles was born into the Assassin Order, devoting his life to the Assassins' cause. William was lived with his wife in the Assassin compound known as "the Farm", located in the Black Hills of South Dakota, near Rapid City. The Farm had approximately thirty Assassins in the compound, William's son Desmond Miles was born and raised there. William trained his son, raising him to be ready to leave at any time should their enemies find them.
In 1998, William was put in charge by another assassin Paul Bellamy to look for information about an individual named Daniel Cross, whom the order assumed was an assassin. William Discovered Daniel Cross was the descendant of Nikolai Orelov, who was closely tied to the Tunguska event. William sent this information to Paul Bellamy, and they accepted Daniel Cross into the brotherhood.
In November 2000, Daniel had located and was personally introduced to the Mentor of the assassin order, It was then revealed that Daniel had an Impulse trigger implanted in him by Abstergo during his youth which lead him to kill the mentor. Daniel then revealed the location of all the assassin compounds to the templars, resulting in the Templars initiating the "Great Purge" to purge these compounds, though the Farm remained well.
Losing their mentor and most of their compounds gone, the Assassins went into hiding, doing their work from remote compounds and cells. At this time, control of the Order was handed to William Miles, And William became leader of the assassins. in 2003, his son Desmond ran away from the Farm compound, believing his parents to be paranoid about the Templars and believing them to be 'conspiracy freaks'. Despite william and the assassins efforts to find Desmond, they were unsuccessful in retrieving him.
William continued to lead the assassin Order however, keeping regular contact with the Assassin cells through their private Email network. by 2012, Lucy Stillman worked undercover for the assassins as the assistant of Warren Vidic, one of the Inner Sanctum of the Templar Order. After her teammate's death, Clay Kaczmarek,"Subject 16", Abstergo's Lineage Discovery and Acquisition division tracked down Desmond Miles, William's son and captured him, using him in the Animus Project as "Subject 17". During this time, William and the other assassins escaped the farm right before a templar attack.
Breaking Desmond out of the Italian Facility Of Abstergo, Lucy and Desmond joined Shaun Hastings and Rebecca Crane to continue looking through Desmond's Genetic Memories to help the assassins this time. William constantly kept contact with Lucy to check on Desmond.
by reliving the memories of his ancestor Ezio Auditore, Desmond attained the location of Ezio's Apple of Eden, hidden away in the Colosseum Vault in Italy. The four of them made it into the First Civilization Vault, upon Desmond touching the apple, his body was taken possession of by Juno, a member of the First Civilization, She forced him to stab his teammate Lucy, killing her. The assassins made it in time to save Desmond, who was placed inside the Animus to save his consciousness using the Black Room.
Desmond relived more of Ezio's memories, finding a stable memory sequence from 1506. Desmond received an e-mail from William to inform him that the memory sequence he needed to complete would lead them to some information that the Assassins needed. by the end of the memories, Leonardo da Vinci and Ezio Auditore found a Vault in Rome, located beneath the Pythagorean Temple. When Ezio activated a pedestal using his hands, the room projected a set of coordinates: 43 39 19 N 75 27 42 W, these led to Turin, New York in America; revealed to be the location of the Grand Temple constructed by the First Civilization.
Upon Completing the sequence. William instructed the other assassin to sedate Desmond, but it was too late; Desmond had fallen into a coma, and entered the Animus's black room, a safety feature to keep him alive. Despite this, William was confident that his son would recover, he and the other assassin left to investigate the Co-ordinates they just found.
Relocating to New York
When Desmond finally woke up from his coma, William greeted him, with Desmond recognizing him immediately. Desmond, seeing the Apple, told his team that he knew what they needed to do, William opened the doors of the van they were in to reveal the Grand Temple outside.
Meanwhile, Abstergo had been tracking William for some time, as they knew he had become the Mentor of the Assassin Order. Upon discovering William's Location, Warren Vidic and Laetitia England assigned their Top Templars to find and eliminate William.