Callum Lynch, a man sentenced to death for murder, wakes up in the Abstergo Foundation after his execution. The facility is a front for the modern-day Templars. Dr. Sofia Rikkin explains to Callum that they are searching for the Apple of Eden, which contains the genetic code for free will. Using the Animus technology, they intend to force Callum into reliving the memories of his ancestor, Aguilar de Nerha, a member of the Assassins during the Spanish Inquisition, to locate the artifact. Callum is skeptical but compelled by the technology that syncs him with Aguilar's genetic memories.

As Callum experiences Aguilar's past, he becomes skilled in the ways of the Assassins. Through the shared memories, he witnesses the fierce battle between Assassins and Templars over the Apple. In the present, Callum's exposure to his ancestor's experiences begins to affect him on a cellular level, enhancing his physical abilities. Meanwhile, Sofia struggles with her father, Alan Rikkin's, methods and the moral implications of their work. The Templars grow restless for results, and Callum finds himself at the center of a centuries-old conflict, with his personal loyalties called into question.