Desmond is captured by Abstergo and forced to use a machine called the Animus to explore Altaïr ibn-La'Ahad's memories during the time of the Third Crusade. Desmond begins to witness events after Altaïr breaks all three tenets of the Assassin Brotherhood while attempting to stop Robert de Sablé from taking a Piece of Eden. Al Mualim, the Brotherhood's leader, demotes Altaïr to Novice and tasks him with assassinating the nine Knights Templars, including de Sablé, to regain his former status. Altaïr's quest eventually leads him to face de Sablé in the presence of King Richard I of England warning the King of de Sablé's plot to kill him. Altaïr defeats de Sablé, but with his last words, de Sablé reveals that there were ten Templars, the last being Al Mualim, who now holds the Piece of Eden. Altaïr returns to face Al Mualim, struggling to fight through the illusions created by the Piece, but eventually kills Al Mualim. When Altaïr recovers the piece, he—and those watching the Animus—witness a holographic map showing locations across the globe where other artifacts are located. Desmond is pulled from the Animus, and was going to be killed, but his life is spared by Lucy Stillman, an Assassin working as a mole within Abstergo, as she claims they might need to further examine his memories later. He comes to learn that a former test subject had left messages only Desmond can see, foretelling of the end of the world in 2012.
The first Assassin's Creed introduced elements that would remain cornerstones of the rest of the series. The game attempts to create historical versions of Masyaf (the Brotherhood's location), Jerusalem, Acre and Damascus, and incorporates a number of documented historical figures into the story. The virtualized Animus system, free running, climbing, stealth, and parkour elements were all present in this title, as well as the initial formulation of the combat system. The player would have to complete a number of side quests before they would be able to obtain an assassin quest from a local Brotherhood guidemaster in each city, though future games would abandon this prerequisite.