Cal reunites with Joseph (now played by Brendan Gleeson). Cal and Sophia discuss the project as they both hate the Assassins as it was they that killed both their mothers. Aguilar performs a Leap of Faith, but it causes Callum in the present to be caught in a malfunction with the Animus. They cause explosions by setting off oil barrels and then run over rooftops as the Templars chase after them.
Benedicto is burned alive, but Aguilar manages to free himself and Maria. The Assassins are set to be publicly executed. Now, Aguilar and Maria are captured and detained in a cell with their mentor Benedicto (Carlos Bardem). He is subdued and taken back to the Animus. Cal dodges Aguilar's attacks, but he ends up striking several Abstergo officials.
Cal experiences more hallucinations, seeing Aguilar attacking him. Rikkin meets with a higher-up, Ellen Kaye (Charlotte Rampling), who wants to shut down Rikkin's project due to the lack of success in locating the Apple. They both claim to be seeking the Apple of Eden in order to rid the world of violence.
Sophia and her father Alan Rikkin (Jeremy Irons) are followers of the Templars. She states that the Animus is meant to show people who made them what they are. Sophia explains that these reflections are normal as part of being put in the Animus. Cal begins to experience hallucinations of Aguilar fighting, at times appearing as though he is attacking Cal. Williams), whose ancestor Baptiste used voodoo against his enemies. Cal meets other people in the facility who are descendants of Assassins, including Moussa (Michael K. Sophia then takes Callum out of the Animus, leaving him on a literal cliffhanger. Aguilar grabs Ahmed and is left dangling before a Templar leader named Ojeda (Hovik Keuchkerian) approaches him.
They run the chariot off the street, causing it to slide over a cliff. Aguilar and Maria chase after a chariot where Ahmed is being taken. Aguilar strikes when he kills the Templar group's leader with a Hidden Blade concealed in his sleeve. He and his partner Maria (Ariane Labed) are tasked with rescuing the son of Sultan Muhammad XII (Khalid Abdalla), Prince Ahmed of Granada (Kemaal Deen-Ellis), who has been kidnapped by Templars under the order of Tomas de Torquemada (Javier Gutierrez) in order to obtain the Apple from the Sultan. After getting hooked into the Animus, Cal finds himself in the Spanish Inquisition as Aguilar. Sophia explains that the Animus will allow Cal to see the memories of his ancestor, Aguilar. Callum is taken to a room with a large claw-like mechanism called the Animus. They need Cal for an important experiment. Sophia tells Cal that the building belongs to Abstergo Industries. Cal runs out of his room and comes across a window overlooking the city in a massive building. Sophia Rikkin (Marion Cotillard), who tells him that he is legally dead, but has been brought to a facility. Cal experiences trippy imagery before passing out. He is hooked up to a chair for a lethal injection. An adult Callum (now played by Michael Fassbender) is headed to his execution after being convicted of murder. Cal runs away from home as his father is pursued by modern day Templars. After he fails, he goes home and finds his mother Mary (Essie Davis) has been murdered by Cal's father Joseph (Brian Gleeson), who is dressed as an Assassin. We are Assassins." We jump to the 20th century where a young Callum Lynch (Angus Brown) trying to ride his bike across rooftops. He recites the Assassin's Creed: "We work in the dark to serve the light. Aguilar de Nerha (Michael Fassbender) is tasked with stopping the Templars from taking the Apple. The Brotherhood of Assassins were the ones set out to destroy the Templars. The Templars wants to seize the Apple for control over free will in a violent world.