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At the CIA headquarters in Langley, Deputy Director Ward Abbot finds out about a failed assassination attempt on dictator Nykwana Wombosi. Meanwhil
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The next morning, he visits a bank using the number that was embedded in his hip, and opens a safe deposit box to find several passports containing his picture (all under different names and nationalities), large amounts of assorted currencies, and a handgun. He assumes the name from the first passport, Jason Bourne. He takes all the passports and money, but leaves the handgun. As he leaves, a bank employee calls the CIA black ops group Operation Treadstone, stating that Bourne has been sighted.
After being chased by police, Bourne escapes into the U.S. Consulate where he is again pursued by authorities. Bourne escapes and finds a woman name Marie, offering her $20,000 to take him to an address in Paris. In the United States, Alexander Conklin, the head of Treadstone, assures Deputy Director Abbott that he will destroy any evidence connecting them to the field agent, Jason Bourne, responsible for the failed assassination attempt on Wombosi. He activates three "assets" to take down Bourne: Castel, Manheim, and The Professor.
Bourne arrives at the address
Soon afterwards, Jason and Marie travel to a train station, where Jason tells Marie to stay in the car while he stores the money in a locker. Marie disobeys and goes to buy some liquor. Jason comes back to the car to find Marie missing, but then sees her heading back from across the street. He yells at her for leaving and tries to do the right thing and go to the police to clear her
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Meanwhile, Conklin plants a body in the morgue in an attempt to fool Wombosi into thinking Kane is dead, but Wombosi recognizes that the body is not his assailant. Using a sniper rifle, The Professor assassinates Wombosi in his home. Bourne investigates the incident and concludes that he was an assassin prior to his amnesia. He and Marie leave the city and travel into the French countryside to stay at the house of Eamon, Marie's brother, where Jason decides that he wants to live a normal life and no longer wants to be who he was.
In the morning, The Professor comes to kill Jason. Bourne uses a shotgun to blow up a propane tank and cloud the view of the sniping Professor. After a brief standoff in a cropfield, Bourne shoots The Professor twice with the shotgun and interrogates him briefly, and The Professor reveals their mutual connection to Operation Treadstone before he dies from blood loss.
Bourne sends Marie away for her own safety. She doesn't want to leave him, having fallen in love with him. He has grown attached to her as well, but he insists. He contacts and meets with Conklin, and plants a tracking device on Conklin's vehicle to discover the location of Operation Treadstone's safe house in Paris. After following the vehicle, he gains access to the Treadstone's safe house where Nicky Parsons and Conklin are.
Bourne holds Conklin and Parsons at gunpoint, and begins to remember his last mission through successive flashbacks. He was on Wombosi's yacht executing his plan to make the assassination look
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Bourne tells Conklin that he is leaving Treadstone and warns him not to try to follow him. Conklin reveals he has a radio in his pocket transmitting. After knocking Conklin unconscious, Bourne leaves Nicky unharmed, has a shootout in the stairwell with several CIA agents, and escapes into the night.
Abbott decides that Treadstone should be closed down for good, and has Manheim assassinate Conklin. Abbott goes before an oversight committee and explains Treadstone as an ineffective assassin-training program, then immediately shifts the focus of the hearing to an idea for a new project codenamed "Blackbriar". Sometime later, Jason finds Marie renting out scooters to tourists in Mykonos,Greece, and the two reunite.