The overall story within Assassin's Creed is set in the near-future, where barkeeper Desmond (the character controlled by the player) has been kidnapped by an unknown person prior to the start of the game, and is brought to the Animus project. The Animus is able to pull out memories from ancestors of the user, allowing the user to replay those memories as if he were there himself. Desmond was "chosen" for the project due to his relationship to his ancestor Altaïr, a member of the Assassins during the Third Crusade of the Holy Land; the researches express interest in understanding more of how the Assassins worked. Though initially Desmond's sub-conscious rejects the memories of Altaïr, he eventually learns to accept them and is able to proceed to follow Altaïr's actions through the Animus.
The memories of Altaïr that Desmond experiences start in AD 1191: Richard the Lionheart has just recaptured the port city of Acre from occupying Muslims. With a base of operations established, the Crusaders prepare to march south. Their true target is Jerusalem – which they intend to recapture for Christianity. However, Saladin, leader of the Islamic army, currently rules the city. Stinging from his army’s defeat at Acre, he will not allow Richard to humiliate him again. The Muslim forces are massing in the ruins of Arsuf, intending to ambush the Crusaders and prevent them from reaching Jerusalem. These war maneuvers have left the rest of the Holy Land wide open. While Richard and Saladin battle one another, the men left to govern in their stead have begun taking advantage of their newfound positions of power. Exploitation, manipulation, and provocation rule the day.
The first memory Desmond experiences is that of Altaïr failing to assassinate the Grand Master of The Templar Knights, Robert de Sable, and recover the order's treasure. Due to this, Altaïr is demoted to Uninitiated (the lowest rank in the Assassin Order). But Sinan, leader of the Assassins, offers him an opportunity to redeem himself. Altaïr must venture out into the Holy Land and assassinate Nine men said to be exacerbating and exploiting the hostilities created by the Third Crusade. In doing so, he will stabilize the region, allowing Sinan to usher in an age of peace.
Along the way, however, he will begin to discover that his targets are bound by more than just a shared interest in personal gain. They share membership in a secret society familiar to the Hashshashin. And they are not simply looking for profit. Their true goal and how they plan to achieve it leads to a modern-day conspiracy with secrets to be discovered during the course of the story.