A bartender named Desmond Miles is captured by Abstergo, a company with strange technology and a sinister plan. They put Desmond into a machine called the Animus, which synchronizes him with memories of his ancestor Altaïr, an Assassin who lived during the Crusades.
Altaïr tries to prove himself by working against an organization known as the Templars. He kills nine officials from that order but learns of a traitor in the Assassin’s own ranks. That man is Al Mualim, the de facto leader of the Assassin Brotherhood.
Altaïr goes after Al Mualim and stops him from using a powerful mind-control device known as a Piece of Eden. Altaïr defeats Mualim but sees many strange things that he cannot explain.
Throughout this story, Lucy Stillman occasionally brings Desmond back to his timeline. Lucy is working as a mole inside Abstergo. She warns him that his memories could uncover something much bigger that threatens not the old world but his own time.
Desmond also learns that the Templar Order is still alive and well in the modern day and that Abstergo is an arm of their hidden power.