NOTE: This spoiler was sent in by Michael.
The movie starts off at night at the end of The Bourne Supremacy with Bourne still in Moscow fleeing from the police (presumably it's right after he confesses to the Russian girl that he killed her parents). The police are in hot pursuit and Jason is limping from the car crash in Supremacy. He breaks into a closed pharmacy so he can get some painkillers for his gunshot wound in his shoulder from the last movie. While he's treating himself, he has a flashback to his training days, and two men are asking him over and over, "Are you committed?" Jason replies, "I can't." At that point, he's grabbed by two men in masks who put a hood over Jason's head and force it under water in a tank. At that point, two Moscow police officers come up behind him and order him to put his hands up. Jason turns around as one officer starts to grab him and quickly knocks him out and steals his gun. He orders the other officer to give him his radio, and Jason smashes it before telling the officer that "my fight isn't with you." Jason leaves.
Six weeks later....
A reporter for the British newspaper The Guardian, named Simon Ross, meets up with a CIA officer named Neal Daniels, who's obviously nervous. Neal tells Simon about a project code-named "Blackbriar", and the person at square one of Blackbriar is Jason Bourne.
Langley, Va, CIA Headquarters
At a meeting with CIA director Ezra Kramer (Scott Glenn), there is a discussion about tying up loose ends. Noah Vosen (David Strathairn) and Pamela Landy (Joan Allen) are there. It is clear that Jason Bourne could be an embarrassment to the CIA and must be found, even though Pamela argues that she doesn't think that Jason is out to burn anybody. Shortly thereafter, the reporter Simon makes a phone call to his boss and mentions the word "Blackbriar", which automatically triggers an CIA alert because they are monitoring all cell traffic around the world. The CIA immediately begins to track Simon when he gets back to London.
Jason Bourne is taking a train to London and is reading Simon's article in the Guardian that talks about the mystery of Marie's death, Jason Bourne, and a possible CIA coverup regarding a secret program called Blackbriar. Bourne calls Simon at his office, but he calls the number of one of Simon's colleagues who comes to fetch Simon to the phone. This is a good thing because the CIA only has Simon's cell tracked and can't listen in on the phone call. Jason tells Simon who he is and to go to Waterloo Station, a very busy commuter train station. The CIA manages to have a man on the street who uses a listening device and hears Simon tell the cab driver where he's going. Noah also activates an "asset" (assassin), to go to the station to get Bourne.
As Simon gets there, Jason buys a cell phone at a kiosk (one of those prepaid ones that has a set number of minutes), walks by Simon without saying anything to him and slips the phone into his coat pocket. He then calls the number and tells Simon to go to a bus stop across the street and stand next to a guy with a blue hat on. All the CIA guys can't listen into the phone conversation (because it's the throwaway one and not Simon's), and they think Simon is talking to the guy with the blue hat. The bus comes, the CIA agents swarm the bus stop and quickly subdue the blue hat guy (who's completely innocent) and take him away. They jump on the bus, too, but Simon has walked away rather than get on the bus per Jason's instructions. Back in Waterloo Station, Jason gives Simon directions on where to walk (guiding him away from the ever present security cameras). But Simon panics when he thinks a garbage sweeper guy is pulling a gun out (he's not), and starts running and is spotted by the real CIA agents. Jason tells him to enter a store and he subdues a couple of the agents, and then a couple more in typical Bourne fashion. The CIA only now realizes that it's Bourne helping Simon (they knew he was getting help to avoid the agents but not from who) when they spot him on a camera. Jason wants to know who Simon's source was for the article in the paper, but Simon is reluctant to give up his source. Jason peers out the store window and ventures out to get away from the station. On the cell phone, he tells Simon not to come out until he gives him the all clear. Noah has now authorized the asset to take both Bourne and Simon out. The asset sets up on a building and the CIA disables the cameras in the station so they won't record the two being shot. But Jason realizes something is wrong when he sees the cameras stop moving. He orders Simon not to come out but Simon again panics and darts out the doorway. The assassin immediately gets a head shot on Simon. As the crowd panics, Jason ducks down and runs to Simon's body, pretending to be a bystander assisting him, but he grabs Simon's notes out of his messenger bag and starts running. The assassin can't get a clear shot but he realizes that Jason is headed directly toward his building, so he breaks down the sniper rifle and begins to hightail it out of there. Bourne almost catches up with him but he gets away.
Later, after reading Simon's notes, he finds the name of a brokerage firm in Spain, so he decides to go down there. At the same time, the CIA discovers that Simon had been in Turin earlier that day. They realize that whoever he talked to was the leaker of Blackbriar, and that it had to be a CIA operative who gave it to him. Noah wants to check every single cell phone call from all the CIA operatives in Europe, but Landy disgustedly tells him that nobody would use their CIA issued phone to set up a meeting to give away that information to a reporter. She correctly suggests that they check to see which phones were turned OFF during that time period, because the person who leaked the info wouldn't want the locator function in the phone turned on. There are three people who had their phones off. After cross checking with items found in Simon's apartment, they determine it is Neal Daniels, who is stationed in Spain at the brokerage firm (a CIA front company). They dispatch agents to get there immediately to apprehend Daniels.
Pamela corners Noah in the office and demands to know what Blackbriar is. He tells her it's an umbrella organization run through his department that is authorized to make renditions (arrest terror suspects and turn them over to friendly nations that have less qualms about using torture), and assassinating targets at their own discretion. Pamela doesn't think this is very smart, but Noah tells her they have to act fast in this day and age to kill terror suspects when they get the chance and not have to wait for approval.
Jason is at the brokerage firm, but Daniels has already skated out of there after he opens his safe and takes out a thick TOP SECRET file folder labeled Blackbriar. While in the office, he finds a picture of Daniels and Dr. Albert Hirsch (Albert Finney), although he doesn't know their names, he has a flashback to his training days, and both men were there at the training facility (the ones asking him if he was willing to commit). As he gets ready to leave, a car pulls up with two agents. Jason hides. The two come in and are on the phone with Noah at his command center in New York. They tell him the safe is open and the files gone. Then they see movement behind a door. They fire some rounds into the door. When they carefully open the door, they see that Jason has taped a flashlight to a floor fan that is rotating back and forth, creating the moving shadow under the door. They don't have much time to digest that fact as Jason pulls some Bourne style punk smashing and knocks them out. He goes to leave and almost shoots Nicky (Julia Stiles). He asks her what she's doing there and she says she was stationed in Spain, after Berlin. As they talk, the phone rings in the office. Nicky picks up and it's Noah. When he finds out it's Nicky he says that they have to do an identity check. He says a code word, and on his computer screen she is supposed to say "ruby" if she is under duress or "everest" if she's okay. After looking at Jason for a second, she says "everest." Noah then asks a subordinate quietly how much time for the B team to get there, and the guy holds up five fingers, or five minutes. Noah tells Nicky to hold the fort and backup would be there in an hour. When she hangs up Jason asks her how much time they really have and she says "three minutes." She tells him she knows where Daniels went, that he wired a lot of money that morning to a bank in Tangiers. He says they can go to the coast and catch a ferry to Morrocco.
They leave and stop at a diner on the way. Nicky tells Jason that Treadstone made guys like him the way they were through breaking them down by torture and mental stress techniques. Jason asks her why she was helping him. She says because it "was tough for her, with him (Jason)," and looks at him intently. He gives her a blank look, and she says, "you really don't remember, do you?" He says no. Obviously, they must have had a romantic relationship at some point.
The CIA activates Desh, a CIA assassin, to get Daniels. They know he is in Tangiers because his passport popped up on the grid when he signed into a hotel. Nicky and Jason also try to track down Daniels. Nicky intercepts the CIA activation order for Desh and knows he's on his way. Jason tells her to text message Desh to meet her at a cafe. She says why, all they'll do if Bourne stops Desh is send someone else. Jason tells her that's not what he wants, he wants to see Desh so he can follow him to Daniels. Desh stops by the cafe and picks up a cell phone on Nicky's table that she gives him as part of the ruse. He thinks she's giving it to him as part of her orders from the CIA, so he's not suspicious. The CIA realizes that Nicky hacked the CIA computer system when she found out they sent Desh, so they text message Desh a picture of Bourne and Nicky to kill them after he's done with Daniels. Noah and Landy have a big fight about Noah ordering Nicky to be killed. Desh spots Jason behind him (they're both riding mopeds). He gets to his kill point and drops a satchel of plastic explosives where he knows Daniels will be driving by. Bourne sees it and tries to stop Daniels from driving by it. But Desh hits the remote and blows up Daniels and Bourne is knocked down and stunned by the blast. Desh sees that he is not moving and goes after Nicky at the cafe. Bourne recovers and hot wires a motorcycle as the police arrive. Because he bolts so fast after the explosion they chase him. There is an extended chase. Nicky starts walking through crowded streets when she sees Desh, figuring out that he must be there to kill her. Bourne is trying to catch up with Desh before he gets her, but he is also being chased on foot by the local police. At one point, Jason grabs an aerosol can off of a vendor's cart and throws it into a barrel that has a fire going in it. The explosion hinders the police for a few minutes.
There is an exciting chase on foot through the crowded streets of Tangiers, with Jason desperately trying to save Nicky. There are numerous jumps from building to building as Bourne is closing in. Ultimately, he catches up with Desh and there is a massive hand to hand combat fight. Most memorably, Bourne grabs a book to fend off Desh using a brass candlestick. He disarms him and shoves the book against Desh's throat, pinning him against a wall while Bourne starts walloping on his face. They end up in a bathroom where Jason gets a choke hold on Desh and finally strangles him. He tells Nicky to use Desh's phone to confirm to the CIA that Desh killed Jason and Nicky. Bourne bribes the morgue guy to let him look at Daniels' blown up briefcase. He finds a scrap of paper giving the New York address of the CIA office. He tells Nicky in the hotel later that she'll have to go on the run. Lots of long looks between them. She dies her hair black and cuts it short in a scene that is very reminiscent of Marie doing the same thing in the Bourne Identity. At one point, Jason looks at her in the mirror, and it seems as if he realizes the similarity. They don't act on it though and he sees her off the next day.
Noah calls CIA director Kramer and tells him they've killed Bourne, but that they're still trying to verify it. Kramer tells him that they're going to try to pin Blackbriar on Pamela if it goes public.
Bourne gets to New York and goes to a building that is empty and is right across the street from the CIA office. In a neat blend of the Bourne Supremacy and Ultimatum, they reenact the same scene at the end of Supremacy in this one. He calls Pamela Landy and says he hears she's been looking for him. She tells him his name is David Webb, and he's from Missouri, and his birth date is 4/15/71 (important later!). Yadda, yadda, yadda, he then tells her to get some sleep...she looks tired. She looks up and realizes he's nearby. All this time, Noah's team has been listening in on the phone. They watch as Pamela leaves the office and follow her, thinking she may be going to meet Jason. He calls her and tells her to meet him at a park nearby. Noah and his whole team go quickly to the park. Bourne calls Noah on the phone and turns on a tape recorder. Noah says they should get together and have a face to face talk.
Jason asks, "where are you?"
Noah says, "In my office."
Jason says, "I doubt it."
Noah says, "Why do you doubt it?"
Jason says, "Because if you were in your office, we'd be talking face to face right now," and hangs up. Noah orders his whole team to go back to the office immediately. Meanwhile, while Jason was on the phone, he was using some special tape to pull up a fingerprint from Noah's desk. He then places it on his floor safe, and pushes the playback button on his tape recorder, which has Noah's voice saying, "Noah Vosen," when he answered his cell phone call from Bourne. The combination voice print and fingerprint opens his safe. Jason grabs the Blackbriar file and puts it in his messenger bag.
There is a huge car chase as Bourne escapes. The short of it is that the assassin in London and Bourne crash their cars. The assassin is stunned and Bourne pulls his gun on him but doesn't shoot. The assassin can only look at Bourne while he decides whether or not to shoot (important later). Bourne leaves him alive.
Bourne figures out that the birthdate that Pamela gave him, 4/15/71, is actually an address. 415 East 71st street. Unfortunately, one of Noah's techs ran Bourne's actual birthday and found it was different. When Noah hears this, he immediately realizes that the address is for Treadstone's training facility. Pamela meets Jason at the door, he gives her the file for her to use and goes in the building. She tries to talk him out of it because she wants him to go with her so they can reveal Blackbriar to the public, but Jason says he is ending this whole thing right now. As he goes in she starts to leave but realizes Noah's men are there, so she darts back into the building and finds a fax machine and starts sending the Blackbriar file to someone.
Jason gets to the top floor and realizes this is the room that he started his Treadstone training in. At that point Dr. Hirsch walks in and starts talking to Jason. Jason demands to know why they forced him to be an assassin. Hirsch tells him he has it all wrong, Bourne volunteered for the job. Jason then has a flashback to him coming there and turning in his dogtags (he's a captain in the military), indicating that the Dr. was right. He then remembers the doctor cajoling Jason into completing his mission. Jason says he doesn't want to, but then asks what the guy did, so it's obvious they are talking about an assassination target. Jason is trying to justify why he should do it. Finally, Jason remembers that he suddenly raised up his gun and shoots a guy three times who's wearing a hood. We then realize that this was his first big test and the whole time the guy was in the room with them while the doctor was trying to convince him to do it.
Jason tells the doctor that his name is David Webb. He says he's not going to kill the doctor because he doesn't deserve to have a star put up on the wall of Langley headquarters (they do that for agents killed in the field). Then Noah's agents start to bust in the door, but Jason leaps out a window. In the ensuing foot chase, he gets to the roof but the assassin from London has the drop on him, and can shoot him any time he wants. But he asks Jason why he didn't shoot him when the car crashed earlier, so Jason realizes he's probably not going to shoot. He starts to jump off the building into the East River from 10 stories up, but Noah reaches the roof at the same time and shoots him in the back.
Jason hits the water and floats motionless underwater. They cut back and forth to a scene of Pamela testifying before the Senate, to Bourne floating motionless, to Noah and CIA director Kramer being arrested, to Bourne floating motionless, to Nicky watching CNN in a lounge area (airport maybe?) and the reporter is saying that the person who started it all, David Webb, has been missing for three months since he fell ten stories into the East River. Nicky starts smiling then, and it switches to Jason suddenly comes to and starts swimming quickly away underwater, so we know that Noah's bullet didn't hit after all.