An unconscious man (MATT DAMON) is pulled from the Mediterranean Sea with two bullet holes in his back. When he comes to, he has no idea who he is, why he ended up in that situation, or how he can speak his rescuers' native tongue. Armed with only a bank account number that was removed from his body along with the bullets, the man heads for Zurich in hopes of solving this mystery.
There, he discovers that his name is Jason Bourne and that he lives in Paris. Yet, the contents of his safety-deposit box also contain various passports with other names, a great deal of money and a gun. After a run-in with American Embassy guards who want to capture him for reasons unknown, he offers to pay a stranger, Marie Kreutz (FRANKA POTENTE), $10,000 to drive him to Paris. She reluctantly agrees and the two eventually arrive in the French capital, only to have a highly trained assassin attempt to kill Jason in his apartment.
Meanwhile, at CIA headquarters in Langley, VA, agent Ted Conklin (CHRIS COOPER) is trying to explain to his superior, Ward Abbott (BRIAN COX), what went wrong with a covert operation. They're also concerned about Nykwana Wombosi (ADEWALE AKINNUOYE-AGBAJE), an exiled African leader, who's writing a tell-all account of the agency's history in his land and is threatening to name names if they don't help return him to power.
As Paris-based operative Nicolette (JULIA STILES) keeps Conklin informed of Wombosi's activities, she does the same regarding Jason and Marie. With Conklin calling in additional operatives, including The Professor (CLIVE OWEN), to take care of both matters, Jason and Marie try to figure out who he really is and why he's obviously so highly trained in spy-related matters, all while avoiding others' various attempts at capturing or killing him.