The book's story follows Altaïr as told by the character of Niccolo Polo. It details the life of Altaïr (An Assassin), beginning with the death of his father. Altaïr watches his father as he's executed for the unintended death of a noble and some time later also watches one of his father's fellow Assassins kill himself out of guilt over the man's death. Altaïr soon begins to train under Al Mualim (Leader of the Assassin Order also known as Mentor Assassin), who instructs him not to tell his fellow Assassin Abbas of his father's suicide. Despite this warning Altaïr tells Abbas, who receives the news poorly. This causes their friendship to become broken which inevitibly leads to problems in the future between the both of them.
The book then progresses to many years later as an older Altaïr, his wife Maria and their son Darim are returning to Masyaf after successfully assassinating Genghis Khan. In their absence Abbas has proclaimed himself Master of the Assassins and taken over Masyaf, ruling the people through fear and violence. Altaïr is met with cool indifference and discovers that despite being told that his son Sef have traveled to Alamut, his son was murdered by Malik. Malik has been imprisoned but claims his innocence. Altaïr breaks him out of jail, planning to confront Abbas and reclaim his place as Master Assassin. These plans are thwarted when Abbas has Malik killed and frames Altaïr for his death. Out of 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. The final chapter shows that Ezio Auditore da Firenze(Da Firenze simply meaning "from Firenze/Florence") is the reader, and he is on a boat arriving in Constantinople, in the second sequence of events in Revelations.

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