Picking up shortly after the first game, Altaïr learns that the surviving Templars plan to flee to Cyprus and infiltrates one of their strongholds in Acre to stop them. Though he fails to prevent their escape, he defeats and captures Maria Thorpe — who had sought to avenge her former master, Robert de Sablé — and, chartering a ship, sails after the Apple of Eden with Maria in tow. In Cyprus he discovers that Armand Bouchart has succeeded de Sablé as Grand Master, and that the Templars, having bought the island from King Richard, have imposed a repressive regime upon its people. Aided by a local resistance movement, Altaïr sets out both to free Cyprus and to locate a hidden Templar "archive" of knowledge and artifacts, cutting down Bouchart's lieutenants — Frederick "the Red," Moloch "the Bull," the twins Shalim and Shahar, and the Dark Oracle — before confronting and defeating Bouchart himself at the archive, escaping just as it collapses.
The game also charts the evolving bond between Altaïr and Maria. At first hostile and biting — calling him "the man who spared my neck but ruined my life" — Maria gradually warms to the assassin who keeps rescuing her from harm despite her repeated escape attempts and never punishes her. In time she chooses to fight at his side, killing a Templar mole within the resistance and standing with Altaïr in the final battle, having fallen in love with him. After their escape from the archive, the two resolve to head east, toward India.