Simon Ross, a reporter from the newspaper The Guardian meets up with Neal Daniels,a CIA officer who tells him about the project called the “Blackbriar”.
Simon calls his boss at the newspaper and tells him about his new story using the word: Blackbriar. This is enough to alert the CIA and they are now after him.
Jason Bourne reads the article from The Guardian that talks about him and the project named Blackbriar. Bourne calls Simon using,the number of one of his colleagues,and asks Simon to meet him at a very busy train station. The CIA with the help of an agent and a listening device hears Simon when he tells the cab driver to head for the Waterloo Station. Vosen activates an assassin in order to get Bourne.
As Simon arrives at the station Bourne walks by him and sleeps a cellphone into his pocket. On this phone Jason gives Simon directions on what to do to escape the CIA surveilance. After Simon manages to get out of the CIA sight Jason orders him to wait until it is safe to come out. At one moment Simon panics,he gets spotted by the CIA assassin and the assassin kills him. In the chaos generated by the shooting Jason grabs Simon` s notes from his bag and runs.
From Simon`s notes Bourne finds the name of a brokerage firm Spain and decides to go there.
The CIA now has to find who was the agent that gave Simon the information concerning the project Blackbriar. They discover that Simon was in Italy recently. After a few investigations they find out that only three of their European agents had their phones turned OFF in that period of time. One of them was Neal Daniels. The CIA immediately recognise that was the leak and sends agents to get him.
In Spain, Bourne realise that he was there to late, because Daniels has already left. He finds a picture of Daniels and Dr. Albert Hirsch and he remembers that they both took part at his training program...When he was about to leave he has to get rid of two CIA agents. At this moment he meets up with Nicky who steps into the office. As the phone rings Nicky picks up and speaks with Vosen. She assures him that everything is OK.
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Nicky tells Bourne that she knows where Daniels is because he transferred a large amount of money to a bank in Tangiers so they head to Morocco.
In Tangiers, CIA activates Desh, another agent, in order to get Daniels. Nicky intercepts the activation order for Desh and Bourne convinces her to message Desh to meet her at a Cafe. Jason must see Desh in order to follow him and find Daniels. At the Cafe, Desh meets up with Nicky and now Jason can follow him. Desh spots Bourne behind him but,even so,he manages to go to the kill point and kill Daniels.
Desh`s mission is now to eliminate Nicky and Bourne because the CIA realised that Nicky hacked into their systems when she intercepted the activation order for Desh. Bourne is chasing Desh,who is going after Nicky at the Cafe. Finally, Bourne catches up with Desh and in the fight that follows manage to kill him and save Nicky. From Desh`s phone Nicky sends to the CIA the confirmation that Jason and Nicky were killed.
At the local morgue, Bourne bribes a man to let him look at the briefcase of Daniels and he finds a piece of paper with the top secret address of a CIA office.
Later, at the hotel, he tells Nicky that she will have to go and hide herself.
Bourne goes to New York and from a building right across the street from the CIA office he calls Pamela Landy. She tells him that his name was David Webb and that he was born in Missouri in April 15 1971. Realising that Bourne is very close because he can see her face Pamela leaves her office hoping that she will have the chance to meet him. Bourne sends her a message to meet in a nearby park.
Noah, with all the team, follows Pamela when Bourne calls him on the phone while recording the conversation. Noah says that they should meet face to face.When Bourne asks him where he is Noah says: “In my office” . “I doubt it” answers Bourne. Noah asks “Why do you doubt it?" "Because if you were in your office, we'd be having this conversation face to face” says Bourne.
With a special tape, Bourne gets a fingerprint from Vosen`s desk and together with the recorded voice of Vosen he is now able to open Noah`s safe. From the safe Bourne takes the Blackbriar file and leaves.
A mad car chase follows and the assassin that killed Simon in London is after Bourne. At some point Bourne has the occasion to kill the assassin but instead of that he decides to let him alive.
Bourne realises that the birth date that Pamela Landy gave him was in fact an address : 415 East 71st street, it was for Treadstone's training facility. Pamela meets Bourne at the entrance,he gives her the Blackbriar file and enter into the building.
Realising that Noah`s men are there, Pamela steps into the building and, from a fax machine, she sends the Blackbriar file somwhere else.
In his way to the top floor of the building Jason recognise the place where he was trained to be a super assassin. Then Dr. Hirsch walks in and starts talking to Jason. Jason wants to know why they turned him into an assassin. Hirsch tells him that he volunteered for the job. A lot of memories are invading Bourne`s memory now. He recalls being a captain in the army, but soon, he also remembers Dr. Hirsch persuading him to complete his first mission,a test. So,the doctor was not entirely right.
Jason tells the doctor that his name is David Webb and the reason for not killing him was that the doctor didn`t deserved to receive a star on the wall of Langley headquarters.
Surrounded by Noah`s men, Bourne gets out on the roof where he meets again with the assassin from London. Because Jason let him live the agent asks why he didn`t shoot him before, in the chase. “Look at what they make you give” answers Jason,then he jumps into the waters of the East River.
Noah and Kramer are arrested and Pamela Landy testifies before the Senate.
A reporter speaks about David Webb, the man who started all, while Nicky watches the news on CNN. The reporter says that his body was never found and Nicky begins to smile.
The movie ends with the image of Bourne swimming into the river.
