Former CIA covert operative Jason Bourne (Matt Damon), eludes Moscow police and goes into hiding after being shot by Russian F.S.B. agent Kirill (in the previous film, The Bourne Supremacy). Six weeks later, Guardian correspondent Simon Ross (Paddy Considine) meets with a source to discuss Bourne and Operation Treadstone. The CIA begin tracking Ross when he mentions "Operation Blackbriar" on a cell phone call to his editor. Bourne travels to Paris to inform Marie's brother, Martin (Daniel Brühl), of her death and assures him he's hunting her killers. In London, Bourne meets with Ross at Waterloo Station after learning of Ross' investigation of Treadstone. When Bourne realizes that the CIA is tracking Ross, he helps him evade capture, but Ross deviates from Bourne's instructions and is sniped by Blackbriar "asset" (assassin) Paz (Édgar Ramírez) on orders from Blackbriar's director Noah Vosen (David Strathairn).
CIA Director Ezra Kramer (Scott Glenn) sends Pamela Landy (Joan Allen), who hunted Bourne six weeks earlier unsuccessfully, to help Vosen after he spots Bourne in a CCTV camera feed. After searching Ross' notes, they surmise that his source was Neal Daniels (Colin Stinton), CIA Station Chief in Madrid, who was formerly involved in Treadstone and is actively involved in Blackbriar. Bourne, having taken Ross' bag after he was killed, is led to Daniels' Madrid office but finds it empty. Nicky Parsons (Julia Stiles), a former Treadstone support technician, arrives shortly after Bourne incapacitates the CIA field team sent by Vosen and Landy to capture him. She decides to help Bourne escape another incoming CIA squad and tells him Daniels fled to Tangiers. It's indicated that Nicky and Bourne had a deep, possibly romantic relationship before he lost his memory.
Upon arriving in Tangiers, Nicky hacks into the CIA database to locate Daniels' location but fails, finding that Blackbriar asset Desh Bouksani (Joey Ansah) has been tasked with killing him. Vosen learns of Nicky's log in attempt and orders Desh to kill her as well as Bourne, a decision Landy disagrees with. Afterwards, Vosen calls Kramer and confirms their intentions to use Landy as the scapegoat if things go wrong. Bourne tails Desh to Daniels but fails to prevent Daniels' death by a planted roadside bomb. He does, however, protect Nicky by strangling Desh after an intense hand-to-hand fight and later sends her into hiding. Upon examining the contents of Daniels' charred briefcase, Bourne finds the address of the deep cover CIA bureau in New York City where Vosen directs Blackbriar.
Bourne travels to New York; Landy receives a phone call (in a repetition of the final scene of The Bourne Supremacy) which is revealed to be tapped by Vosen. Landy thanks Bourne for the tape he sent her which revealed the corrupt dealings of former Treadstone director Ward Abbott, and also provides him that his real name is David Webb and his birthdate is 4/15/71. While speaking with Landy, Bourne notices Vosen storing highly classified materials in a safe in his office. Bourne tells Landy to "get some rest" because she "looks tired", which she and Vosen both understand to mean that he's currently surveilling her. Vosen then intercepts a text message sent to Landy from Bourne advising a location for a meet and leaves his office with a team to follow her. Bourne breaks into Vosen's office and steals classified Blackbriar documents and Vosen sends Paz after him, resulting in a car chase which ends with Paz forcing Bourne's stolen police car into a concrete divider. Bourne gets out and holds Paz at gunpoint before sparing his life and continuing on to 415 East 71st Street, memories of which were triggered by the false birthday he was given by Landy. Vosen also figures out Landy's code and warns Dr. Albert Hirsch (Albert Finney), who ran Treadstone's behavior modification program, that Bourne is en route.
Landy meets Bourne outside the building and admits to her change of heart; that she's helping him because she hadn't signed up for programs like Treadstone and Blackbriar. Bourne gives her the Blackbriar files before going inside and Landy faxes them to a secondary witness with Vosen arriving just as the last page is successfully sent. Bourne meets with Hirsch in an upper level room and, with Hirsch's help, finally recollects that he was not forced into the program, but in fact volunteered. He proclaims to no longer be "Jason Bourne" and flees from Vosen's pursuing team to the roof. There, Paz confronts Bourne with why he didn't kill him when he had the chance. Bourne questions Paz as to his motives and repeats the dying words of "The Professor", a Treadstone assassin he killed years earlier (in The Bourne Identity): "Look at us... Look at what they make you give." Paz lowers his gun as Bourne runs to jump off the roof, but Vosen appears and shoots at Bourne as he leaps into the East River below. Some time later, Landy is shown testifying against Blackbriar before the Senate. Nicky watches a television news broadcast about the exposure of Operation Blackbriar, the arrests of Hirsch and Vosen, a criminal investigation against Kramer for authorizing the operation, and that David Webb, a.k.a. Jason Bourne, was reportedly shot and fell into the East River. Upon hearing that his body has not been found after a three-day search, Nicky smiles; Bourne is shown swimming away underwater after his fall.
Cast
Matt Damon as Jason Bourne/David Webb, former top operative for the black ops Operation Treadstone. Bourne takes on the task of finding out who made him what he was and why.
Julia Stiles as Nicky Parsons, Bourne's former Treadstone contact in Paris. She is the only character besides Bourne and Marie Kreutz (who only appears in flashbacks in The Bourne Ultimatum) to appear in all three films.
David Strathairn as Noah Vosen, CIA Deputy Director in charge of the new Treadstone black ops upgrade called Operation Blackbriar, and the film's principal antagonist. He considers Bourne a threat to the operation and sets out to kill him.
Joan Allen as Pamela Landy, CIA Deputy Director and Task Force Chief, sent in to aid Vosen in tracking down Bourne. No-nonsense and tough as nails, she later proves to be Bourne's key ally.
Albert Finney as Dr. Albert Hirsch
Scott Glenn as Ezra Kramer, Director of the CIA
Colin Stinton as Neal Daniels, CIA Station Chief in Madrid
Joey Ansah as Desh
Edgar Ramirez as Paz
Tom Gallop as Tom Cronin, Pamela Landy's assistant
Corey Johnson as Ray Wills, Vosen's deputy at Operation Blackbriar
Franka Potente (uncredited) as Marie Helena Kreutz, Bourne's murdered girlfriend
Daniel Brühl as Martin Kreutz, Marie's half brother
Scott Atkin as Agent Kiley
Paddy Considine as Simon Ross, a reporter for London's Guardian newspaper.
