Callum Lynch (Michael Fassbender) wakes up before his execution and finds that he has been selected by Sofia (Marion Cotillard) to participate in a program that can free humans from violent impulses. The virtual reality machine Animus allows users to experience the memories of their ancestors. After being tied to the machine, Callum Lynch realizes that he is a descendant of Aguilar, an assassin who lived during the Spanish Inquisition. They are looking for the Apple of Eden that can control free will. Under pressure from her father Allen (Jeremy Irons), Sofia reluctantly manipulates Callum Lynch to go back in time to find the whereabouts of the Apple of Eden in the modern world, threatening his physical and mental health. But after fellow killer Musa (Michael Williams) hinted to Callum Lynch and reminded him that Allen might have impure motives, Callum Lynch began to reconsider his actions and motives, and the fate of human free will became unresolved...