The movie begins before the end of the events in The Bourne Supremacy, as Bourne, wounded by a gunshot from the Russian assassin Kirill, is still evading the Moscow police. Cornered by two officers while breaking into a medical clinic to treat his wounds, Bourne overpowers the officers, knocking one out, while holding the second at gunpoint. He leaves them alive as he escapes, saying in Russian: My argument is not with you.
Six weeks later, Simon Ross, a security correspondent for The Guardian, meets
with someone in Turin, to discuss Treadstone. Bourne goes to Paris to tell Marie's brother, Martin, of her death, then heads to London. Bourne then reads an article in The Guardian by Ross about Bourne, Treadstone, and "Operation Blackbriar." He then arranges to meet Ross in London at the south entrance of Waterloo Station. Ross, however, is under surveillance because his use of the word "Blackbriar" in a phone call to his editor was tracked by ECHELON, alerting the CIA. CIA section chief Noah Vosen alerts his staff at the Anti-Terrorism Deep Cover in New York to find out any information on Ross, believing that Operation Blackbriar has been compromised.
After receiving a call from Bourne, Ross takes a taxi to Waterloo Station. At the station, Bourne sees CIA officers f
ollowing Ross and places a prepaid mobile phone on him; through it, Bourne instructs him on how to dodge the station's surveillance. However, Vosen orders an assassin, Paz, to kill Ross and his source. Vosen's team identifies Bourne on a security camera and recognizes him as the original Treadstone assassin, and assumes he is Ross's source. While Paz gets into position with a sniper rifle, Bourne tells Ross to remain hidden, but Ross panics and steps out into the open, allowing Paz to deliver a clear kill shot. In the chaos, Bourne grabs Ross's notes, revealing his source as Neil Daniels, the Madrid CIA station chief.
Deputy Director Pamela Landy is asked to help capture Bourne. With Landy's help, Vosen and his team also determine that Neil Daniels is Ross' source. They send a team to Daniels' office in Madrid, but Bourne arrives first, finding one photograph of familiar faces he has rec
ently been having flashbacks of in an otherwise empty safe, as Daniels has already left. Bourne attacks the CIA team members when they enter the office. Right after Bourne secures the room, Nicky Parsons then enters it unexpectedly. Nicky tells him that she was reassigned to Madrid after Berlin, and that Daniels has fled to Tangier. She helps him escape the CIA reinforcements by telling Vosen that Bourne had already left the office. Her motivation for helping Bourne isn't entirely clear, but it is subtly implied that before he lost his memory, they had been in a relationship. While in Tangier, they discover the CIA has sent assassin Desh Bouksani to eliminate Daniels. Nicky uses her official clearance access to send Desh a message, telling him to meet her for a new phone, thus allowing Bourne to follow Desh to his target. When Vosen realizes Nicky's deceit he orders Desh to kill Nicky and Bourne after terminating Daniels. Landy is outraged at Vosen's willingness to indiscriminately kill CIA personnel and quits the operation.
Bourne follows Desh and is unable to save Daniels, who dies from Desh's planted bomb. When Desh returns f
or Nicky, Bourne outruns the Tangier police and attacks Desh. After a brief, intense fight, Bourne eventually strangles him. Bourne has Nicky code in the fact that the both of them are dead to give each of them a head start at disappearing. Bourne then puts Nicky on a bus with the advice to run and hide, saying, "It gets easier" (Referring to blending in and disappearing). At the Tangier morgue, Bourne examines Daniels' charred papers and finds the address of the CIA substation in New York City. Bourne takes a flight to New York City, and on arrival deliberately uses a passport that alerts Landy to his presence. Bourne calls Landy while observing her and Vosen from across the street, the same call that was shown at the end of The Bourne Supremacy. Bourne sends a text message to Landy to arrange a meeting. Vosen and his team intercept the message and follow Landy as she leaves the building. However, the meeting is simply a diversion to allow him to enter Vosen's office and steal classified Blackbriar documents.
Vosen recognizes the diversion too late after receiving a phone call from Bourne to get a recording of his voice, which is one of the keys to unlocking his Blackbriar safe. Bourne reveals he is in Vosen's office, and Vosen frantically orders CIA officers back to his office to capture Bourne. But Bourne escapes and enters into a car chase with CIA officers and Paz. Bourne eventually incapacitates Paz in the chase, but despite having a clear shot, refrains from killing him. Just outside the Treadstone facility, Bourne meets Landy and gives her the stolen doc
uments from Vosen's office before entering the building. On his way back to his office, Vosen eventually works out that Landy gave Bourne the address of the Treadstone R&D facility in code when Landy gave Bourne his date of birth. Vosen calls Dr. Albert Hirsch to warn him of Bourne' impending arrival at facility, and then races to the facility where Landy finishes faxing away the Blackbriar document that Bourne stole to the FBI. She looks at Vosen and says, "You better get yourself a good lawyer." Bourne meets with Dr. Albert Hirsch, who ran Treadstone's psychological conditioning program. Bourne was their first, experimental conditioning subject. With his help, Bourne remembers that, as Captain David Webb, he volunteered for the program and killed a man in the same room. Horrified by the memory of what he did to complete his conditioning and to assume the Jason Bourne identity, he tells Hirsch, "I remember everything. I'm no longer Jason Bourne."
Hirsch asks if Bourne will now kill him, but Bourne replies in the negative, saying "You don't deserve the star they'd
give you on the wall at Langley." Bourne jumps out a window when CIA agents barge into the room. After a short chase to the roof Paz holds Bourne at gunpoint and demands to know why Bourne spared his life. Bourne stares at Paz, and after a long pause says, "Do you even know why you're supposed to kill me?....Look at us. Look at what they make you give," repeating the dying words of the Treadstone assassin called The Professor from The Bourne Identity. Paz lays down his weapon as a sign of friendship, but Vosen appears and fires at Bourne just as he jumps from the roof into the East River below. He appears to be shot, and falls into the water rather than diving.
Images of Bourne's unmoving body floating in the river are interspersed with ima
ges of Nicky watching a news report, sometime later, noting the exposure of Blackbriar, the arrests of Hirsch and Vosen, the newsflash that Ezra Kramer is the subject of a United States Senate hearing regarding his conduct, and that David Webb, alias Jason Bourne, was shot and fell into the East River but his body has not been recovered, even after a three-day search, at which point Nicky smiles realizing that Bourne is still alive. In the final moments of the film, Bourne's limp, drifting body springs to life and he is shown swimming away in the East River.
Six weeks later, Simon Ross, a security correspondent for The Guardian, meets
with someone in Turin, to discuss Treadstone. Bourne goes to Paris to tell Marie's brother, Martin, of her death, then heads to London. Bourne then reads an article in The Guardian by Ross about Bourne, Treadstone, and "Operation Blackbriar." He then arranges to meet Ross in London at the south entrance of Waterloo Station. Ross, however, is under surveillance because his use of the word "Blackbriar" in a phone call to his editor was tracked by ECHELON, alerting the CIA. CIA section chief Noah Vosen alerts his staff at the Anti-Terrorism Deep Cover in New York to find out any information on Ross, believing that Operation Blackbriar has been compromised.After receiving a call from Bourne, Ross takes a taxi to Waterloo Station. At the station, Bourne sees CIA officers f
ollowing Ross and places a prepaid mobile phone on him; through it, Bourne instructs him on how to dodge the station's surveillance. However, Vosen orders an assassin, Paz, to kill Ross and his source. Vosen's team identifies Bourne on a security camera and recognizes him as the original Treadstone assassin, and assumes he is Ross's source. While Paz gets into position with a sniper rifle, Bourne tells Ross to remain hidden, but Ross panics and steps out into the open, allowing Paz to deliver a clear kill shot. In the chaos, Bourne grabs Ross's notes, revealing his source as Neil Daniels, the Madrid CIA station chief.Deputy Director Pamela Landy is asked to help capture Bourne. With Landy's help, Vosen and his team also determine that Neil Daniels is Ross' source. They send a team to Daniels' office in Madrid, but Bourne arrives first, finding one photograph of familiar faces he has rec
ently been having flashbacks of in an otherwise empty safe, as Daniels has already left. Bourne attacks the CIA team members when they enter the office. Right after Bourne secures the room, Nicky Parsons then enters it unexpectedly. Nicky tells him that she was reassigned to Madrid after Berlin, and that Daniels has fled to Tangier. She helps him escape the CIA reinforcements by telling Vosen that Bourne had already left the office. Her motivation for helping Bourne isn't entirely clear, but it is subtly implied that before he lost his memory, they had been in a relationship. While in Tangier, they discover the CIA has sent assassin Desh Bouksani to eliminate Daniels. Nicky uses her official clearance access to send Desh a message, telling him to meet her for a new phone, thus allowing Bourne to follow Desh to his target. When Vosen realizes Nicky's deceit he orders Desh to kill Nicky and Bourne after terminating Daniels. Landy is outraged at Vosen's willingness to indiscriminately kill CIA personnel and quits the operation.Bourne follows Desh and is unable to save Daniels, who dies from Desh's planted bomb. When Desh returns f
or Nicky, Bourne outruns the Tangier police and attacks Desh. After a brief, intense fight, Bourne eventually strangles him. Bourne has Nicky code in the fact that the both of them are dead to give each of them a head start at disappearing. Bourne then puts Nicky on a bus with the advice to run and hide, saying, "It gets easier" (Referring to blending in and disappearing). At the Tangier morgue, Bourne examines Daniels' charred papers and finds the address of the CIA substation in New York City. Bourne takes a flight to New York City, and on arrival deliberately uses a passport that alerts Landy to his presence. Bourne calls Landy while observing her and Vosen from across the street, the same call that was shown at the end of The Bourne Supremacy. Bourne sends a text message to Landy to arrange a meeting. Vosen and his team intercept the message and follow Landy as she leaves the building. However, the meeting is simply a diversion to allow him to enter Vosen's office and steal classified Blackbriar documents.Vosen recognizes the diversion too late after receiving a phone call from Bourne to get a recording of his voice, which is one of the keys to unlocking his Blackbriar safe. Bourne reveals he is in Vosen's office, and Vosen frantically orders CIA officers back to his office to capture Bourne. But Bourne escapes and enters into a car chase with CIA officers and Paz. Bourne eventually incapacitates Paz in the chase, but despite having a clear shot, refrains from killing him. Just outside the Treadstone facility, Bourne meets Landy and gives her the stolen doc
uments from Vosen's office before entering the building. On his way back to his office, Vosen eventually works out that Landy gave Bourne the address of the Treadstone R&D facility in code when Landy gave Bourne his date of birth. Vosen calls Dr. Albert Hirsch to warn him of Bourne' impending arrival at facility, and then races to the facility where Landy finishes faxing away the Blackbriar document that Bourne stole to the FBI. She looks at Vosen and says, "You better get yourself a good lawyer." Bourne meets with Dr. Albert Hirsch, who ran Treadstone's psychological conditioning program. Bourne was their first, experimental conditioning subject. With his help, Bourne remembers that, as Captain David Webb, he volunteered for the program and killed a man in the same room. Horrified by the memory of what he did to complete his conditioning and to assume the Jason Bourne identity, he tells Hirsch, "I remember everything. I'm no longer Jason Bourne."Hirsch asks if Bourne will now kill him, but Bourne replies in the negative, saying "You don't deserve the star they'd
give you on the wall at Langley." Bourne jumps out a window when CIA agents barge into the room. After a short chase to the roof Paz holds Bourne at gunpoint and demands to know why Bourne spared his life. Bourne stares at Paz, and after a long pause says, "Do you even know why you're supposed to kill me?....Look at us. Look at what they make you give," repeating the dying words of the Treadstone assassin called The Professor from The Bourne Identity. Paz lays down his weapon as a sign of friendship, but Vosen appears and fires at Bourne just as he jumps from the roof into the East River below. He appears to be shot, and falls into the water rather than diving.Images of Bourne's unmoving body floating in the river are interspersed with ima
ges of Nicky watching a news report, sometime later, noting the exposure of Blackbriar, the arrests of Hirsch and Vosen, the newsflash that Ezra Kramer is the subject of a United States Senate hearing regarding his conduct, and that David Webb, alias Jason Bourne, was shot and fell into the East River but his body has not been recovered, even after a three-day search, at which point Nicky smiles realizing that Bourne is still alive. In the final moments of the film, Bourne's limp, drifting body springs to life and he is shown swimming away in the East River.