In the Mediterranean Sea, fishermen rescue an American adrift with two gunshot wounds in his back. They tend to his wounds and find he has no memory of his identity, but retains his speech, advanced combat skills and fluency in several languages. The skipper Giancarlo (Orso Maria Guerrini) finds a laser projector under the man's hip that gives the number of a safe deposit box in Zürich. The Skipper gives him some money. Upon landing in Imperia, Italy, 2 weeks later, the American goes to the bank in Switzerland to investigate the deposit box. He finds it contains money in various currencies, passports and identity cards with his picture on them, and a handgun. The man takes everything but the gun, using the name on the American passport, Jason Bourne (Matt Damon).After Bourne's departure, a bank employee contacts Operation Treadstone, a CIA black ops program. Treadstone's head, Conklin (Chris Cooper), issues alerts to police to capture Bourne and activates three agents to kill him: Castel (Nicky Naude), Manheim (Russell Levy), and the Professor (Clive Owen). CIA Deputy Director Abbott (Brian Cox) contacts Conklin about a failed assassination attempt against exiled African dictator Wombosi. Conklin promises Abbott that he will deal with the Treadstone agent who failed. Wombosi is an African dictator who was deposed by the CIA. He is threatening to a write and expose CIA ops in Africa, unless he is re-instated.Turns out CIA has a covert assassination program called Treadstone & Bourne is an agent. He failed in one of his missions and now CIA wants to eliminate him to tie loose ends. Conklin is the CIA guy & Abbot is his boss.Bourne tries evading the Swiss police by using his U.S. passport to enter the American consulate, but is pursued by Marine guards. He escapes the consulate, offering a German woman, Marie Kreutz (Franka Potente), $20,000 to drive him to an address in Paris listed on his French driving license. At the address, an apartment, he hits redial on the phone and reaches a hotel. He inquires about the names on his passports there, learning that a "John Michael Kane" was registered but died two weeks prior in a car crash. Castel ambushes Bourne and Marie in the apartment, but Bourne gets the upper hand. Instead of allowing himself to be interrogated, Castel throws himself from a window to his death. Marie finds wanted posters of Bourne and herself and is panicky, and agrees to help him. After Bourne evades Paris police in Marie's car, the two spend the night in a Paris hotel.Wombosi (Adewale Akinnuoye-Agbaje) obsesses over the attempt on his life. Conklin, having anticipated this, planted a body in Hoffenmein morgue, Paris to appear as the assailant, but Wombosi is not fooled (since the body had no bullet holes in the back) and threatens to report CIA secrets to the media. The Professor assassinates Wombosi on Conklin's orders. Conklin tells Abbott that Bourne killed Wombosi to complete his mission and might report back in 24 hrs. Meanwhile Jason gets Marie to investigate the hotel where Kane was registered and finds the morgue where his body is kept. But the body has already been moved and that the day before Wombosi visited the morgue to see Kane's body.Bourne, posing as Kane at a security company, learns about Wombosi's yacht (which was in the company's brochure), and that the assailant was shot twice in the back during the escape; he realizes he was the assailant. He and Marie take refuge at the French countryside home of Eamon (Tim Dutton) and his children. Eamon is Marie's relative, but Marie and Jason don't know that all of Marie's relatives are under surveillance.Under pressure from Abbott to tie off the Wombosi matter, Conklin tracks Bourne's location and sends the Professor there, but Bourne shoots him with Eamon's shotgun, mortally wounding him. The Professor reveals their shared connection to Treadstone before dying. Bourne sends Marie, Eamon, and Eamon's children away for their protection, then contacts Conklin via the Professor's phone. Jason tells Conklin that Marie is dead as she was slowing him down. Conklin tells Abbott that its too late to bring Jason in. Conklin agrees to meet Bourne, alone, in Paris. When Bourne sees Conklin has not come alone he abandons the meeting, but places a tracking device on Conklin's car, leading Bourne to Treadstone's safe house in Paris. Conklin has ordered the moving of the safe house..Bourne breaks in and holds Conklin and logistics technician Nicolette "Nicky" Parsons (Julia Stiles) at gunpoint. Bourne and Conklin's conversation at the safe house clears much of the mystery. Bourne asks, "Who am I?", to which Conklin replies, "You're US government property. You're a malfunctioning $30 million weapon! You are a total goddamn catastrophe!"When Conklin presses him to remember his past, Bourne recalls his attempt to assassinate Wombosi through successive flashbacks. As Kane, and working under orders from Treadstone, Bourne infiltrated Wombosi's yacht and got close enough to assassinate him. However, Bourne was unable to kill Wombosi while his children were present, and instead fled, being shot during his escape. Bourne announces he is resigning from Treadstone and is not to be followed. As agents descend on the safe house, Bourne fights his way free. When Conklin leaves the safe house, he encounters Manheim, who kills him under Abbott's orders. Abbott then shuts down Treadstone, and lets Bourne walk away since Conklin was the one who messed up..Abbott reports to an oversight committee that Treadstone is "all but decommissioned" before discussion turns to a new project code-named "Blackbriar". Bourne finds Marie renting out scooters to tourists on Mykonos, and the two reunite.