The Animus allows Desmond to relive the "genetic memories" of his ancestor, , a master assassin in the year 1191. Abstergo’s goal is to locate a powerful artifact known as a Piece of Eden (specifically the Apple of Eden) that they believe Altaïr once possessed. The Historical Story (1191) Altaïr's journey is one of failure and redemption:

: After killing Robert de Sablé, Altaïr learns the ultimate truth—his own master, Al Mualim , was a secret collaborator with the Templars. Al Mualim used Altaïr to eliminate his rivals so he could keep the Apple of Eden's mind-controlling power for himself. The Conclusion

: The story begins at Solomon’s Temple, where Altaïr, arrogant and overconfident, breaks the three tenets of the Assassin’s Creed while trying to retrieve the Apple of Eden from Templar Grand Master Robert de Sablé . His failure results in the death of a fellow assassin and his own demotion to the rank of novice.

In the modern day, Desmond is pulled out of the Animus. Abstergo now has the map they need. However, because of the "Bleeding Effect"—a side effect of prolonged Animus use—Desmond begins to see through Altaïr's eyes in the real world. He discovers cryptic messages written in blood on his room walls by a previous test subject (), hinting at the end of the world in 2012. Are you planning to play the sequels, or

In the modern setting, a bartender named is kidnapped by Abstergo Industries , a powerful pharmaceutical company that is actually a front for the modern-day Templar Order . Under the supervision of Dr. Warren Vidic and his assistant Lucy Stillman , Desmond is forced into a machine called the Animus .

: As Altaïr eliminates his targets, he discovers a common thread: they were all members of the Templar Order working with Robert de Sablé to unite the Holy Land through control rather than faith.

: To regain his rank and honor, Altaïr’s mentor, Al Mualim , tasks him with assassinating nine influential men across the cities of Acre, Damascus, and Jerusalem . These men, Al Mualim claims, are profiting from the Third Crusade and causing suffering.

Altaïr returns to the Assassins' stronghold in and defeats Al Mualim. Upon Al Mualim’s death, the Apple activates, projecting a holographic map of the world that reveals the locations of other Pieces of Eden scattered across the globe.