Salah Al'Din lays siege to Masyaf. In response, Al Mualim sends Altaïr's father, Umar Ibn-La'Ahad, to leave a marker on his pillow while he sleeps, to encourage Salah Al'Din to retreat. Umar succeeds, but is forced to kill a passing noble during his escape. The next morning, Salah Al'Din agrees to retreat, but only if the man responsible for the death of the noble is delivered to him for execution. When Al Mualim refuses, Salah Al'Din brings out an Assassin spy he had discovered, Ahmad Sofian, intending to kill him in Umar's place. Unwilling to let someone else die for his mistake, Umar gives himself up and is executed while his son watches.
Later, after mourning his father for some time, a young Altaïr is woken in the middle of the night by Ahmad standing over his father's desk. Ahmad, haunted by the death of his fellow Assassin, apologizes to Altaïr before slitting his own throat. Al Mualim takes Altaïr and Abbas, Ahmad's son, under his wing to train as Assassins, instructing Altaïr never to tell Abbas of his father's suicide. Abbas is told that his father ran from Masyaf in the middle of the night. The two orphans grow close and learn the ways of the Brotherhood quickly, however, one night Altaïr tells Abbas the truth about his father. Abbas is furious and during a training practice, accuses Altaïr of lying to shame him and forces him at knifepoint to say that he was lying. Their friendship is irreparably broken. Abbas begins to stumble down the path to bitterness and shame, while Altaïr begins to grow arrogant and haughty.
After the events of the two games, Altaïr, his wife Maria and their son Darim are returning to Masyaf after successfully assassinating Genghis Khan. Altaïr and Maria are now in their sixties and are beginning to feel the effects of their age. In the ten years they have been gone, Abbas has proclaimed himself Master of the Assassins and taken over Masyaf. He now rules the people through fear and violence. Altaïr is met with cool indifference and demands to know where his younger son, Sef, is. One of Abbas' lackeys, Swami, informs him that Sef, his wife and his two daughters have gone to Alamut for reasons unknown. Darim goes in search of his brother, while Maria and Altaïr stay in Masyaf to speak to Abbas. However, Abbas tells them that Sef is dead, murdered by Malik. Later that night, Altaïr sneaks into the dungeon and finds Malik, who professes to be innocent of Sef's murder. Altaïr breaks him out of jail and brings him to Maria to nurse back to health. Altaïr plans to confront Abbas and reclaim his place as Master Assassin, but his plans are thwarted when Abbas has Malik killed and frames Altaïr for his death. In his anger, Altaïr uses the Apple of Eden to kill the man responsible for Sef's death, but also inadvertently causes Maria's death as well. Devastated by the loss of his son and his wife, Altaïr flees Masyaf.
Years later, a merchant named Muhklis is saved from desert bandits by Altaïr, now an old man in his seventies. Muhklis takes an injured Altaïr back to his home in Masyaf and agrees to help him reclaim his place. They hope to take back Masyaf with as little bloodshed as possible. They are joined by a few young men who are against Abbas and are training in the traditional ways of the Assassins, which have been ignored during Abbas' reign. They, along with the people of Masyaf, storm the castle, fighting through Abbas' men, but only killing if absolutely necessary. Altaïr faces Abbas for the last time, killing him with his pistol shot weapon. With the death of their leader, Abbas' men lay down their arms and Altaïr is proclaimed the leader of the Assassins