In the year 2012, a seemingly ordinary bartender named Desmond Miles was abducted by a mysterious organization. The captors attach Desmond to a strange device called "Animus", which allows him to access the memory of his ancestor, an assassin named Altaïr. For some reason, the reconstruction of Altaïr's memories is vital to the captors.

After accessing Altaïr's memory, Desmond is able to experience the events that took place in the Holy Land in the year 1191, the time of the Third Crusade. Al Mualim, the leader of the assassins, orders Altaïr to kill nine prominent historical figures, who supposedly let war and corruption take over the Holy Land.