Present-day protagonist Desmond Miles has fallen into a coma from the events of the previous game. To save Desmond's mind, he is placed in a specialized area of the Animus called the Black Room. Upon awakening inside the Animus, in a location called Animus Island, he meets the consciousness of Subject Sixteen, who occupied the Animus before him. Sixteen explains that Desmond's mind is broken, and the only way for him to repair it is to play through his ancestors' stories until there is nothing left for them to show Desmond, at which point the Animus can separate Desmond from Ezio and Altaïr, and awaken Desmond from his coma.
Desmond enters Animus Island's memory portal, which places him back in the perspective of Ezio Auditore. Ezio has traveled to the former Assassin's fortress in Masyaf to unlock secrets Altaïr had previously discovered, and find the true purpose of the Assassins. Upon arriving, he finds Masyaf taken by the Templars, who mark him for death. Ezio escapes to the bowels of the castle, where he discovers the entrance to Altaïr's library. He learns that five disc-like "keys" are required to unlock the door; that the Templars have one underneath the Ottoman Sultan's palace; and the rest lie hidden in Constantinople, part of the Ottoman Empire.He travels there and is greeted by Yusuf Tazim, leader of the Turkish Assassin Order, and befriends a young student named Suleiman. Ezio learns that the keys were hidden in the city by Niccoló Polo. While searching for the old Polo trading post, Ezio encounters and befriends Sofia Sartor, a young Italian traveler and book collector, and quickly becomes infatuated with her. Sofia helps Ezio discover the locations of the remaining keys, while keeping his intentions and position a secret from her.
Meanwhile, Constantinople is in chaos due to conflicts between Prince Ahmet and his brother Selim, who are quarreling over who will inherit the Sultanate. Caught in the middle of the conflict, Suleiman reveals to Ezio that he is an Ottoman prince, and that he suspects the Templars are behind the feud. Ezio uncovers evidence that Manuel Palaiologos, with Templar support, is attempting to raise an army to overthrow the Ottomans and reestablish the Byzantine Empire. Ezio kills Manuel and recovers the final key, only to discover that Ahmet is the true mastermind of the Templar plot to open Altaïr's library.
During these events, Ezio uses the keys in his possession to witness Altaïr's life after the events depicted in the first game. After killing Al-Mualim, Altaïr took possession of the Apple of Eden and assumed leadership of the Assassins. One of the Assassins, Abbas, did not support Altaïr due to past events, and for killing Al Mualim. When Altaïr and his wife Maria left Masyaf for 10 years to repel the Mongol invasion, Abbas staged a coup d'etat, seizing control of the Assassins and executing Altaïr's youngest son Sef. Altaïr sought revenge; but as Maria tried to stop him, Altaïr's rage was felt by the Apple of Eden and killed Maria. Altaïr was forced to flee with his elder son, Darim, and went into self-imposed exile for 20 years. Altaïr finally returned to Masyaf, killed Abbas, then took his rightful place as the Assassins' leader. In the process, Altaïr told the dying Abbas the truth of the latter's father's death. Years later, an aged Altaïr encodes his memories on the five keys Ezio would find, entrusting them to Niccoló.
In Constantinople, Ezio discovers that Ahmet has killed Yusuf and kidnapped Sofia, demanding the keys in exchange for her life. Ezio agrees, but immediately gives chase upon ensuring Sofia's safety. He recovers the keys, but before he can deal with Ahmet, Selim arrives with his armies and executes Ahmet himself, after saying that their father "made his choice."Due to his son Suleiman's endorsement, Selim has Ezio leave Constantinople, warning him never to return again. After completing this memory, the Animus begins to delete excess data—including Animus Island. Sixteen sacrifices himself to prevent Desmond from being deleted by the Animus.
Ezio and Sofia return to Masyaf, where Ezio uses the keys to unlock Altaïr's library. He finds it empty except for Altaïr's skeleton and a sixth key. He discovers that the library was not meant to hold books—rather, it was a vault meant to house Altaïr's Apple of Eden. Through the key, Ezio learns that Altaïr had sealed himself inside to preserve its secret from the Templars. Ezio leaves this Apple in the library, saying "I have seen enough for one life." He then begins talking directly to Desmond, not knowing exactly who (or where) he is, but knowing that he is watching. He tells Desmond of his intention to retire from the Assassins, believing he has served his purpose. He expresses hope that Desmond will be able to find answers to the questions he and Altaïr had worked so hard to uncover.
Suddenly, Desmond is approached by Jupiter, a member of the First Civilization. He explains that the First Civilization had built numerous vaults to study methods to save the planet from destruction. All of the data collected was transmitted to a central vault, where the data was tested. None of the methods were effective, however, and they failed to stop the solar flare from destroying their civilization. Jupiter tells Desmond that he has the power to save the planet from a second solar flare, showing him the location of the central vault. Desmond then wakes from the Animus to see Rebecca, Shaun, and his father William standing over him. They had managed to smuggle him out of Rome, and had taken him to the central vault. Desmond then tells the other Assassins that he knows what to do.Underground, the central vault activates
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