NOTE: Some movies need detailed spoilers, some don't. I received many for this film but kept waiting for the right one. Finally, Brentage5000 came through and here is his detailed spoiler. But first, he says... "Yet another recent sequel that is better than the original. I am definitely liking this trend."
The movie starts with Jason Bourne (Matt Damon) remembering -- through dreams -- some flashes of his past. We see a photo of a family (parents and a young girl) and some flashes of road signs, plus a short bit of his old boss Conklin (Chris Cooper) telling him that, "Trainings over." Bourne wakes up in his bedroom in India where his girlfriend Marie (Franka Potente), the girl who helped him throughout the first movie, comforts him a little and suggests he write it down in his journal. He responds by saying that it never helps but she thinks that eventually he'll have to remember something good. He just looks at her and says that yes, he does remember something good. They go back in and later we do indeed see him writing in his journal.
Meanwhile, in Berlin, we see a man known as Kirill (Karl Urban -- Eomer in Lord of the Rings) watching two men through a sniper scope. We then follow the two men -- along with Agent Pam Landy (Joan Allen), who is watching from Washington -- as they break into a building and begin stealing some old files and a rather considerable amount of cash, having blown open a safe in the wall to get to it. Just as they're getting ready to leave Kirill comes in, kills them both, takes the files and money, plants a print on the safe, and leaves. In Moscow, we see Kirill deliver the files and money to Uri Gretkov (Karel Roden), a high ranking Russian government official. He gives Uri the money and files and is told that he'll get the rest as soon as he completes his assignment: kill Jason Bourne.
Next morning (or the morning after, or two mornings later, or the morning before -- who can tell with all these time zone changes?), we see Bourne running down the beach while Marie looks at a book of clippings Jason has collected of various assassinations that have happened that he may or may not have been involved in (meaning committed). The book ends with a big page listing some names and one big question -- WHO AM I? Later, we see Maria doing some shopping in the street market while Bourne keeps running. As he is taking a break from running to get some water, he spots Kirill, who landed earlier and is now following him. Instinctively he runs for home, gets in his jeep, and hightails it to the market, where he gets Maria and tells her, "We're blown." She piles into the jeep and they start driving, followed by Kirill, who spotted their rather fast moving jeep some ways back.
Bourne begins loading his gun to kill Kirill and he tells her he has no choice. She looks at him and says "yes you do have a choice" meaning that he could choose to stop killing. (Important later). That is the last thing she says to him of any substance.
They duck through some kind of field and make it to a bridge but Kirill, who has been shooting at them, manages to shoot Marie (who was driving) which makes the car go flying off the bridge and into the deep river. Bourne tries to break out but doesn't have much luck at first. Eventually he gets the door open, goes to the other side, gets Marie's door open and finds that she's dead. He leaves her body there in a real tender scene that has her just floating and standing there and makes for the surface. Kirill, meanwhile has looked at everything and safely believes that he has completed his mission. He goes to Moscow, tells Uri this, gets the money, and leaves. Right about this time, in Washington, Pam and her team are finding out that the one print they were able to find on the safe belongs to none other than--but the trail dead ends there, for access to the name of the owner of the print requires access to Project: Treadstone, something no one there has ever heard of.
Back in India, Bourne is now burning all of Marie's fake passports and other documents. He is about to burn a picture of the two of them being happy together when he changes his mind and throws that in his pocket. He goes inside, grabs a gun and his own passports, and starts driving. At the same time, Pam is over at Langley trying to get the level-5 access she needs for her little project. The guy she talks to, CIA Director Martin Marshall (Tomas Arana) gives her the access, which has all the info on Bourne, Conklin, and Treadstone, among other things. This prompts Pam to set up a meeting with Ward Abbott, (Brian Cox) the former head of Project: Treadstone who is currently stationed in London. There, Abbot recalls (for Pams sake, and perhaps the audience's) the events which transpired in the first film while we simultaneously see Bourne himself arriving in Naples. Next, we see a brief meeting between Pam, Abbott, Marshall, and some other agents who say nothing of import, where the connection between Bourne and the murders is outlined for all to see. During the meeting, some underling pokes his head in with the news that, "Jason Bourne just showed up on the grid in Naples." This makes Marshall send both Pam and Abbott to Naples with the instructions to kill Jason Bourne.
Meanwhile, over in Naples, some passport trouble has caused Bourne to be detained in an interrogation room by airport security. A man comes in to question him, but for all the response he gives Bourne might as well be a statue...until a call from Pam alerts the interrogator to Bourne's identity (no pun intended). The guy hangs up and Bourne is in motion, knocking out the guard and beating up the other guy. Bourne cracks open the guys phone, downloads everything from it, including records of recent calls, and puts it all on his phone. He steals the interrogator's car and listens to a conversation where Pam says that Bourne killed two people. He has recorded this and listens to it over and over again while headed for Berlin and the local CIA HQ there. On the way, he experiences more memory flashbacks, including a quick bit of a man and a woman in a room and the picture again. He wakes up from it abruptly in a gas station parking lot somewhere.
Meanwhile,we see Nikki (Julia Stiles) from the first movie, walking down a street in Amsterdam. She is headed somewhere when she is interrupted by Abbott, who throws her in a car and takes her to the headquarters. Pam asks her questions about what she did for Treadstone and some of the other members, and we learn that Treadstone was basically a training ground for blackops murderers and assassins. From there they head for Berlin, bringing Nikki along with them. Meanwhile, in Munich we see a man arrive home from work and go into his house. He puts his keys on the table, heads for the pantry in the kitchen...and pulls out a gun and aims it at a just revealed Bourne. Bourne says that he emptied the gun, which doesn?t really surprise the guy (another member of Treadstone) because, "...it felt light." Bourne asks why they're after him (Bourne) but the guy doesn't know and says that Treadstone was shut down and Conklin is dead. They fight for a little bit and it ends with the other guy getting choked to death and Bourne setting the guys place on fire before finally heading for Berlin.
In Berlin, Bourne starts calling local hotels looking for the one that Pam is staying in. Through calling her cell number (which he got from the interrogators call-back) while having the clerk at the hotel call her room, Bourne figures out which room she's staying in (he peeked over the counter at the room-calling device). Bourne goes to the floor above, watches her leave from a balcony, and then tails her to the headquarters. While she lays out a plan for getting Bourne, he sets up with a gun and scope across the street. Just as she finishes talking, Bourne calls her and asks why they're after him, but they don't know anymore than him, and Pam slowly begins to realize that maybe they shouldn't be after him. Regardless, she still wants him brought in, so Bourne asks them to use Nikki. Pam asks what she should do if she can't find Nikki, but Bourne assures Pam that she'll find Nikki. When Pam asks where, Bourne says, "She's right next to you."
The next day, Nikki is waiting in a crowded square to meet with Bourne. Watching over her are four snipers and four watchmen from four rooftops (you figure out the setup). Pam and Abbott are watching from HQ and listening over the wire Nikki is wearing. Some protestors for something come out and Nikki gets a call from Bourne telling her to get on a train. She does, and some other agents attempt to follow her through the thickening crowd. Nikki gets in the same car as Bourne, on the other end, and the other two get a few cars behind. Just as the crowd is at it's thickest, Bourne comes up behind Nikki and forces her off the train, telling her that they should have left him alone, either not knowing about the wire or not caring or talking to Pam and Abbott. Regardless, Bourne "escorts" Nikki to a closet in a subway and questions her about what's been happening, and through tears of pain she tells him that they didn't do it, and they have no idea what's going on, and they aren't after him. He asks what his first job was, saying it was in Berlin, but she disputes that, even though she gets hit some more for doing so. Furious and disappointed, Bourne leaves.
Some time later, Abbott is approached by a couple of different agents. One tells him that they found Nikki in the subway station, alive but hurt, but she'll be alright (I'm sure he cares). The other takes him to the safe that was broken into back at the beginning of the movie. He shows Abbott how the charges were not set perfectly, which makes the agent think that Bourne didn't do this and is being set up by someone. Abbott asks the agent to show him again...and then sticks a knife in the guys back (no, really...he literally does that, leaving the dead body behind for someone else to find). Meanwhile, Bourne has stumbled upon a hotel called the Hotel Brecker, which he recognizes from his memory flashes. He goes inside and asks for a room, then says, "Actually, is room 645 available? I've stayed there before." The clerk says that it isn't, but 644, located just across the hall, is. Bourne says that that's acceptable and he heads for the room just as a wanted fax with his picture on it comes in. Bourne breaks into the room, walks through it, enters the bathroom...and remembers Conklin sending him in there to kill a man, but the man's wife is there. She finds Bourne hiding in the bathroom, and Bourne ends up killing both of them, knocking over a picture of the two with their then three-year-old daughter.
While Bourne has been strolling down memory lane, the German police have surrounded and broken into room 644. Bourne hears them and starts climbing for the street. He starts walking, but then a cop car recognizes him, and they chase him through a subway station, and across some tracks, but Bourne loses them by jumping onto a garbage ferry and then climbing back onto another bridge. The cops report the loss, which gets back to CIA, which prompts Abbott to call Uri, who is sounding somewhat suicidal over this whole messy affair. Abbott tries to tell Uri that he will get Bourne, but is hung up on just as Bourne steps out of the shadows. An unsurprised Abbott pretty much confesses everything while Bourne holds him down with what we think is a gun (and strangely, the way Abbott confesses sounds like Stryker confessing everything to Wolverine in X2 -- same actor, y'know) and tells Bourne to kill him, but Bourne just says, "She wouldn't have wanted me to," and slams down a tape recorder next to Abbott's head. Bourne leaves, and sometime later Landy comes looking for Abbott. Abbott tells her that he's sorry, and then proceeds to shoot himself in the head, leaving behind the tape in an evidence envelope marked for her.
Some days later, in Moscow, we see Kirill enjoying himself in a strip club. He goes outside and finds Uri in his car waiting there. Uri tells Kirill that Bourne is still alive. Elsewhere, we see Bourne arriving in Russia. He goes to a phone book and gets an address for someone, then heads for a group of cabbies. One of them is willing to take his American dollars and drives him to the Neski's old house. It's abandoned, but an old neighbor tells him where the Neski girl now lives, in some downtown village. Bourne heads for his cab but it has pulled away after the driver got a call from the train station telling him that his client was a wanted man. Bourne takes off running but soon finds himself being shot at by Kirill from up high...who then finds himself being assaulted by cops...until they discover that he is Russian secret service. The chase resumes, and Jason ducks into a station grabbing some booze and towels to provide a little improptu first aid. As soon as he's got his stuff, Jason steals a cab from some driver and pulls out five seconds ahead of Kirill. Kirill in turn steals someones Jeep -- while they're in it -- and takes off after Bourne. The two chase each other for a matter of time until Bourne manages to get Kirill's car in front of him and slams it against the barricade. He creeps up to the car with his pistol drawn to find that Kirill is badly injured, bleeding and covered in broken glass, but alive. Bourne stands with the gun aimed at Kirill, who moans but does not open his eyes, and Bourne does not shoot to finish him off, but leaves him alive, keeping a promise to Marie that he mentioned to Abbott (she wouldn't want me to).
Bourne grabs his stuff and heads for that village, where he finds the apartment belonging to the daughter of those people he killed. She thinks he's there to rob or rape her, but instead he tells her that her mother didn't kill her father (which is how he made it look). Instead, he killed them, and he is sorry about it, but he's not sure which will be harder -- knowing that he killed them, or knowing that she lived under a lie, and as he leaves, he says he's sorry for that too.
Some time later, in New York City, we see Pam working in an office when her cell phone rings. She picks it up and finds Bourne on the other end. They talk, and she thanks him for the evidence. Just as he's about to hang up, she tells him that she found some information about him in one of the Treadstone files, and she says that his real name is David Webb, his birthday is April 15, 1971, and he's from Newsome, Missouri. He thanks her, and she says that maybe they could get together and talk about it some. He just smiles and says, "Get some rest, Pam. You look tired."