In 1492 Andalusia, during the Granada War, Aguilar de Nerha is accepted into the Assassins Brotherhood. He is assigned to protect Prince Ahmed de Granada from the Knights Templar. In 1986, adolescent Callum “Cal” Lynch finds his mother killed by his father, Joseph, a modern-day Assassin. Gunmen led by Alan Rikkin, CEO of the Templars’ Abstergo Foundation, arrive to capture Joseph, who convinces his son to escape.
In 2016, Cal is sentenced to death for murdering a pimp, but his execution is faked by the Abstergo Foundation, which then takes him to their research facility in Madrid. He is told that the Templars are searching for the Apple of Eden, in order to eliminate violence by using the Apple’s code to control humanity’s free will. Sofia, Alan’s daughter and the head scientist, reveals that Cal is a descendant of Aguilar, the last person confirmed to be in possession of the Apple. She puts Cal in the Animus, a machine which allows him to relive (and the scientists to observe) Aguilar’s genetic memories, so that Abstergo can learn what he did with the Apple.
In 15th-century 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. Cal is quickly pulled out of the Animus by Sofia.
Cal encounters other Assassin descendants held captive at the facility, most of whom are suspicious of his motives, with the exceptions of Lin, the descendant of a 16th-century Chinese Assassin known as Shao Jun; and Moussa, the descendant of an 18th-century Haitian Assassin named Baptiste and a key leader. Cal begins experiencing hallucinations, dubbed “the Bleeding Effect”, of both Aguilar and Joseph. Cal and Sofia build a rapport during their sessions; she confides that her mother was likewise murdered by an Assassin, sharing his hatred of the Brotherhood of which his father is a member.
Back in the Animus, Aguilar and Maria are scheduled for execution at an auto da fe but he manages to free them, leading to a rooftop chase in which they escape through an Assassin “Leap of Faith”. Cal’s mind reacts violently to the session and he is temporarily paralyzed. When Cal learns that his father is also at the facility, he confronts Joseph over his mother’s death. Joseph informs him that the Bleeding Effect will allow modern Cal to possess Aguilar’s combat abilities. He also learns that his mother was an Assassin, and she chose to die by Joseph’s hand rather than be forced into the Animus. Unconvinced, Cal vows to destroy the Assassins by finding the Apple. Meanwhile, Alan is pressured by a Templar Elder, Ellen Kaye, to shut down the multibillion-dollar Animus Project because they have already “won … people no longer care about their civil liberties … they’re content to follow”, leading Sofia to question her father’s true intentions.
Reaffirmed by his encounter with his father, Cal willingly enters the Animus once again, whereupon Aguilar and Maria ambush a meeting between Muhammad and Torquemada. They succeed in killing the Templars and retrieving the Apple, though Ojeda captures Maria in order to force Aguilar to surrender it. Instead, Maria chooses death, and stabs herself on Ojeda’s blade. Aguilar kills him and escapes through another Leap, the force of which causes the Animus to violently malfunction. Aguilar gives the Apple to Christopher Columbus, who promises to take it to his grave. When Moussa and the modern Assassin prisoners start a riot in order to escape, Alan orders the facility purged. Abstergo security kills Joseph and most of the other prisoners.