"Desmond Miles can be considered to be the true protagonist in Assassin's Creed.
The story starts off with flashes of Altair in an odd cloudy room. After about five minutes, Desmond wakes up to find himself on top of a machine and two figures with lab coats near him. He has no recollection of getting to where he is now and is told that he is being held captive. When he questions why, the answer he receives is somewhat unbelievable.
The people in the lab coats are Dr. Lucy Stillman and Dr. Warren Vidic. They run the Animus project for Abstergo Industries. The Animus is a device used to extract genetic memory from an individual about their ancestors. According to Dr. Vidic, the memories of our past relatives are stored in our DNA.
Desmond is told that he has information that someone needs. While Desmond claims to be nothing more than a bartender, it is alluded to that he is an assassin, or at least was one at some point in the past. Moreover, his ancestors were assassins. There is a specific memory in the life of his ancestor Altair that the Doctors are trying to access, but Desmond's subconscious mind is blocking access to the memory and they need his help to access it. If he refuses to assist them, they threaten to retrieve the memory in a more forceful way that will kill Desmond."