In 1492, during the Granada War, Aguilar de Nerha is accepted into the Assassins Creed Brotherhood. He is assigned to protect Prince Ahmed de Granada. In 1986, Callum returns home to find his mother killed by his father, Joseph, a modern-day Assassin. As gunmen led by Alan, CEO of the Abstergo Foundation, the modern day Templar front, approach to capture Joseph, the latter convinces the former to escape.
In 2016, Callum 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. Sophia, 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 Sophia.
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 Sophia build a rapport over their sessions; and confides with Callum that her mother was likewise murdered by an Assassin.
Back in the Animus, Aguilar and Maria are scheduled for execution, but he manages to free himself and her, leading to a rooftop chase in which they perform a "Leap of Faith" (see below) to escape. Callum's mind reacts violently to the session; and he is temporarily paralyzed. He then learns that Joseph is also present at the facility. Confronting Joseph for his mother's death, Callum is informed that as a result of the Bleeding Effect, his and Aguilar's memories are merging, allowing Callum to tap into Aguilar's combat abilities; he also learns that Callum's own mother was an Assassin who chose to die by Joseph's hand, rather than be subjected to the Animus by the Templars. Callum vows to destroy the Assassins Brotherhood by finding the Apple. Meanwhile, Alan is pressured by his superior, Ellen Kaye, to shut down the Animus Project due to its lack of results, leading Sophia to question Alan's true intentions.
Callum willingly enters the Animus once again, whereupon Aguilar and Maria ambush a meeting between Muhammad and Ojeda. They succeed in killing the Templars and retrieving the Apple, though Ojeda captures her in order to force Aguilar to surrender it; but she chooses death, and Ojeda fatally stabs her before Aguilar kills him. He then escapes, performing another Leap, the force of which causes the Animus to violently malfunction. Aguilar then gives the Apple to Christopher Columbus, who promises to take it to his grave. Meanwhile, Moussa and the other Assassin prisoners start a riot in order to escape. Alan orders the facility to be purged, resulting in Joseph and most of the prisoners being killed by Abstergo security.
Callum stands in the Animus chamber and is met with the projections of a number of his Assassin ancestors, including Aguilar, Joseph, and the former's mother. Callum fully embraces his Assassins' creed and, having fully assimilated Aguilar’s memories and abilities, joins Moussa and the surviving Assassins in escaping the facility.
Having retrieved the Apple, Alan and his followers then converge in a Templar sanctuary in London to perform a ceremony. Inside the sanctuary, a disillusioned Sophia meets with Callum, who has come to take the Apple; and she reluctantly allows him to act. Callum sneaks behind Rikkin and kills him to retrieve the Apple, whereupon the Assassins depart, vowing to once again protect it. Sophia vows revenge upon Callum.
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