The film opens with the unconscious form of Jason Bourne floating around in the Mediterranean Sea, 30 kilometres south of Marseilles in France. Some fishermen rescue him and the doctor on board extracts two bullets from Jason's back and a small light emitting diode gadget from his hip which projects an account number in a Zurich-based bank.
Jason spends the rest of the film trying to regain his memory, starting at the bank. His bank box contains heaps of money, six passports with different identities (e.g. Greek, Brazilian, Russian, etc...) and a gun. He is unaware that he is a trained assassin based in Paris as part of the Treadstone Project. As far as US defence officials are aware, Treadstone is an advanced army training programme. However, it is, in fact, a mafia-like unit designed to eliminate internationally "dangerous" people. When his employers find out that instead of being dead at the bottom of the sea, he is still alive, he becomes a target because he could reveal the true identity of Treadstone. The head of Treadstone deploys other assassins in Europe to kill him.
At the US embassy in Zurich, he meets Marie, who drives him to Paris and travels round with him. The head of Treadstone goes to France to meet him. Jason survives the assassination attempts, gives Marie money and tells her to leave for her security, finally gets his memory back, quits Treadstone and goes to find Marie, who now runs a scooter hire company.