Two years after their disappearance, Jason Bourne and Marie Kreutz are in Goa, India. Still experiencing flashbacks about his life as a CIA assassin, Bourne records them in a notebook.
In Berlin, a CIA agent working for Deputy Director Pamela Landy is paying $3 million to an unnamed Russian source for the “Neski files”, documents on the theft of $20 million seven years prior. The deal is interrupted by Kirill, an agent for Russia’s Federal Security Service who works for oligarch Yuri Gretkov. Beforehand, Kirill plants two explosive devices on the building’s electrical circuit. One takes out the power to the building, the other does not go off but has Bourne’s fingerprints planted on it in order to frame him. Kirill kills the agent and the source and steals the files and money. Gretkov directs Kirill to Goa to kill Bourne; however, Bourne spots him at the market and on the beach and flees with Marie in a vehicle. Kirill follows in a car chase and kills Marie instead of Bourne, unaware they had swapped seats in the vehicle. Bourne leaves Goa and travels to Naples.
After finding Bourne’s fingerprint, Landy asks Director Ward Abbott about Operation Treadstone, the defunct CIA program to which Bourne belonged. She tells Abbott that the CIA agent who stole the $20 million was named in the Neski files. Some years previously, Russian politician Vladimir Neski was about to identify the thief when he was killed by his wife in a suspected murder–suicide in Berlin. Landy believes that Bourne and Treadstone’s late supervisor, Alexander Conklin, were somehow involved and that Bourne killed the Neskis. Both Abbott and Landy go to Berlin to capture Bourne.
In Naples, Bourne allows himself to be identified by security. He subdues his CIA interrogator and copies the SIM card from his cell phone. From the subsequent phone call, he learns about Landy and the frame-up. Bourne goes to Munich to visit Jarda, the only other remaining Treadstone operative. Jarda informs Bourne that Treadstone was shut down after Conklin’s death, and tries to incapacitate him. Bourne kills Jarda in self-defense, escaping before the CIA arrives. Bourne follows Landy and Abbott as they meet former Treadstone support technician Nicky Parsons to question her about Bourne. Believing the CIA is hunting him again, Bourne calls Landy from a nearby roof. He demands a meet-up with Nicky and indicates to Landy that he can see her in the office.
Bourne kidnaps Nicky in Alexanderplatz and learns from her that Abbott was the head of Treadstone, not Conklin. Bourne spares Nicky after revealing she knows nothing about the mission since it was not documented. Bourne then visits the hotel where the killing took place and recalls more of his mission—he killed Neski on Conklin’s orders, and when Neski’s wife showed up, he shot her, making it look like a murder–suicide.
Danny Zorn, Conklin’s former assistant, finds inconsistencies with the report of Bourne’s involvement with the death of the agent, explains his theory to Abbott by indicating Bourne’s fingerprint that were on the bomb had not gone off. Abbott kills Zorn to prevent him from informing Landy. Bourne breaks into Abbott’s hotel room and records a conversation between him and Gretkov that incriminates them in the theft of the $20 million. Abbott admits to Bourne that he stole the money, authorized him to murder Neski, ordered Kirill to retrieve the files, and have Bourne framed before arranging for him to be silenced in Goa. Abbott expects Bourne to kill him, but Bourne refuses – believing Marie’s wishes not to kill – though leaves his gun on the table. After Bourne leaves, Landy confronts Abbott about her suspicions and he commits suicide. Landy returns to her hotel room, finding an envelope containing the tape of Abbott’s conversations with Gretkov and Bourne.
Bourne travels to Moscow to find Vladimir Neski’s daughter, Irena. Kirill, tasked once again by Gretkov with killing Bourne, finds and wounds him. Bourne flees in a stolen taxi and Kirill chases him. Bourne forces Kirill’s vehicle into a concrete divider. Bourne walks away, leaving a seriously wounded Kirill. Gretkov is arrested. Bourne locates Irena and confesses to murdering her parents.
Later in New York, Bourne calls Landy; she thanks him for the tape, reveals to him his original name, David Webb, and date of birth, and asks him to meet her. Bourne says, “Get some rest, Pam. You look tired.”