In 1492, during the Granada War, Aguilar de Nerha is accepted into the Assassins Brotherhood. He is assigned to protect Prince Ahmed de Granada. In 1986, Callum Lynch returns home to find his mother killed by his father, Joseph, a modern-day Assassin. As gunmen led by Alan Rikkin (Jeremy Irons), CEO of the Abstergo Foundation, the modern day Templar front, approach to capture Joseph, the latter convinces his son to escape.
In 2016, Callum (Michael Fassbender) is sentenced to death for suspected murder, but is rescued from execution by the Abstergo Foundation, which fakes his death, and transports him to their facility in Madrid, Spain. He is told that the Templars are searching for the Apple, which contains the genetic code for free will, in order to subjugate the human race. Sofia (Marion Cotillard), Alan’s daughter and the head scientist, reveals that Callum is a descendant of Aguilar and conscripts him to the Animus, which allows him to relive Aguilar’s genetic memories so that Abstergo can learn the current whereabouts of the Apple.
In Andalusia, Spain, Aguilar and his partner Maria are deployed to rescue Ahmed, who has been kidnapped by the Templar Grand Master Tomas de Torquemada, to coerce Ahmed’s father, Sultan Muhammad XII, to surrender the Apple. Aguilar and Maria intercept the Templars, but are overpowered and captured by Torquemada’s enforcer Ojeda just as Callum is pulled out of the Animus by Sofia.
In captivity, Callum befriends other descendants of Assassins, led by Moussa, the descendant of an 18th-century Haitian Assassin named Baptiste, and begins experiencing hallucinations, dubbed “the Bleeding Effect”, of both Aguilar and Joseph. Callum and Sofia build a rapport over their sessions; she confides with Callum that her mother was likewise murdered by an Assassin.