A man who may or may not be Jason Bourne (Matt Damon) is found floating in the Mediterranean Sea and is hauled onto a fishing boat. When the ship's doctor examines the unconscious castaway, he discovers two bullet wounds and an implanted device that displays a Swiss bank account number. With nothing but this code, the amnesiac Bourne travels to Zurich and gains access to a safe-deposit box containing a gun, thousands of dollars in various currencies, and valid passports from numerous countries - each listing a different identity. Within minutes, Bourne is on the run from a seemingly ever-present agency, relying on language and fighting skills he didn't even know he possessed!

Offering $20,000 for a ride to Paris, Bourne gains the reluctant help of the nomadic Marie (Franka Potente). Meanwhile, the shadowy organization, headed by a tough-talking bureaucrat (Chris Cooper), sends numerous assassins (including the Professor, played by Clive Owen) after Bourne and Marie. As their situation grows more perilous, the two strangers struggle to find out who Bourne really is and why they are being hunted...