Wounded to the brink of death and suffering from amnesia, Jason Bourne is rescued at sea by a fisherman. With nothing to go on but a Swiss bank account number, he starts to reconstruct his life, but finds that many people he encounters want him dead. However, Bourne realizes that he has the combat and mental skills of a world-class spy—but who does he work for?

An unconscious man is washed ashore on the beach of a small French village during a heavy storm. A retired doctor takes care of the unconscious stranger. When the mysterious man recovers, he can't remember a thing...he does not know his name, he does not know where his flashback memories come from, and he does not know why the access code for an anonymous Swiss bank account is implanted in his thigh. As he seeks his own identity, things quickly become dangerous. There are attempts to kill him, he is well known in first class hotels across Europe, and worst of all, there are strange similarities between his memories and reported actions of the notorious terrorist, Carlos the Jackal.

Bourne is brought out of hiding once again by reporter Simon Ross who is trying to unveil Operation Blackbriar, an upgrade to Project Treadstone, in a series of newspaper columns. Information from the reporter stirs a new set of memories, and Bourne must finally uncover his dark past while dodging The Company's best efforts to eradicate him.

A CIA operation to purchase classified Russian documents is blown by a rival agent, who then shows up in the sleepy seaside village where Bourne and Marie have been living. The pair run for their lives and Bourne, who promised retaliation should anyone from his former life attempt contact, is forced to once again take up his life as a trained assassin to survive.