After a botched undercover mission, a CIA operations leader finds evidence that Bourne was responsible for killing their agents. He's not, but those who framed him also want to tie up loose ends and send an assassin played by Karl Urban to track him down and kill him. He survived their initial encounter but his beloved Marie was killed in the process.
Angry and wroth with revenge, Bourne comes out of hiding to find the people who killed her and bring them to justice, and to also start making amends for past wrongs. This brings him into direct conflict with the remnants of Treadstone, from Berlin to Moscow.
This film is followed by The Bourne Ultimatum.
This film provides examples of:
- Action Film, Quiet Drama Scene: Bourne's apology to Irena Neski following the big car chase in Moscow.
- Badass Normal: Kirill as an FSB agent and freelance assassin is the closest to a normal person among all the super operatives that Bourne has fought yet came the closest of anyone in killing Bourne.
- Batman Gambit: Bourne deliberately gets himself detained at Naples, anticipating that the right people would pick up on it. When they do, Bourne taps their phone conversations and learns their identities and probable locations, making tracking them easier.
- Burn Baby Burn: Bourne burns Marie's passport and photographs after her death, except for one.
- Cassandra Truth: Thanks to Abbott's antics, just about everyone believes that Bourne is coming to eliminate all of Treadstone of his own accord, even though he pleads ignorance to everything that's happened in his disappearance post-Identity and just wants to be left alone. Similarly, Bourne doesn't believe the Treadstone agents in that the operation was shut down.
- When Bourne notices Kirill looking out of place with the locals, he grabs Marie and start to drive them out of town. He frantically tells Marie someone is after them, but Marie is worried about him simply being paranoid, which is the last thing she conveys before she's immediately shot dead by Kirill.
- Death by Adaptation: In the original novels Marie lived to the end of the series (although she was kidnapped in The Bourne Supremacy). Here she's Stuffed into the Fridge in the first act.
- Deceased Fall-Guy Gambit: Abbott tries to pin the Berlin assassination and the money theft on Conklin, who'd died in Identity, and Bourne, who was to be killed before the CIA could find him.
- Dramatic Irony: Pamela Landy yelling at her team that they had absolute control over Bourne's life for decades, should be several steps ahead of him and won't be going home until they find Jason Bourne. When Bourne calls Landy's cellphone, the room is immediately a flurry of activity as they set up traces and try to find out where he is. Meanwhile, at the exact same moment, he's set up a sniper rifle to target them immediately across the street and is watching every move they make.
- Engineered Public Confession: Jason tricks Ward into revealing the truth by holding what seemed to be a pistol, but was actually a tape recorder.
- Happy Ending Override: After the first film Borne could settle down with his girlfriend and live a normal life. Until he dragged back in and his girlfriend is killed.
- Have You Told Anyone Else?: Danny Zorn pre-emptively fulfils this trope by explaining to his soon-to-be murderer Ward Abbott that he has yet to share the damaging information he's found.
- Heal It with Booze: After being shot, Bourne stumbles into a market and grabs several bottles of vodkas and a map, so he can attend to his wound and navigate the hell out of there while being car-chased by a world-class assassin.
- Improv Fu: Jason Bourne can beat the shit out of you with a rolled up magazine and blow up a condo with it when he's done killing you. It should be noted that this example isn't theoretical or exaggerated; it's something Bourne actually does.
- In Name Only: This film has even less to do with the plot of the corresponding novel than The Bourne Identity did: in The Bourne Supremacy, Marie was kidnapped in China but escaped, and Jason spent most of the book looking for her. Also, they were married, and Jason had learned his real name, David Webb, at the end of the first book.
- Info Dump: Landy looking through Treadstone files helps explain the aftermath of Identity to new viewers.
- Inspector Javert: Pamela Landy.
- It Works Better with Bullets: Bourne found Jarda's gun and emptied its bullets. Jarda noted how the gun felt light.
- Leave Behind a Pistol: Bourne does this for Ward Abbott.
- Off Bridge, onto Vehicle: Bourne jumps from a bridge onto a barge during the foot chase in Berlin. This gets his leg injured, as he has a limp for the remainder of the film as a result, though he still manages to escape from his pursuers. The barge is slow and the cops quickly call it to stop, so Bourne just sneaks out by climbing underneath the bridge.
- Possession Presumes Guilt: Jason Bourne remembers assassinating a Russian politician and his wife and making it look like a murder-suicide by placing the gun he used in one's hand.
- Posthumous Character: Everything that happens traces back to the assassination of Vladimir Neski, who'd been killed before revealing that Yuri Gretkov was using stolen CIA funds to buy up Russian oil leases. Jason soon uncovers that he was the one that killed Neski, in his very first Treadstone assignment.
- Precision F-Strike: Bourne himself delivers a powerful one at the end of an intense interrogation he uses on Nicky Parsons. Considering how calm and stoic Bourne usually is in the second and third movies, it really signifies his emotional turmoil and hate for the CIA after losing Marie, the one person he came to really care for, all because Ward Abbott refused to leave him alone and sent an assassin to take him down, but ended up killing her instead by accident.
- Reality Ensues: Hypertrained as he is, Bourne is still only a man; when he leaps from a bridge onto a barge to escape the police, he injures his leg and has a limp for the rest of the film.
- Roaring Rampage of Revenge: The whole movie, albeit so cold and machine-like it seems he's lost his humanity until he spares Nicky after her interrogation, refuses to kill Ward Abbott and when he speaks to Irina Neski.
- Stuffed into the Fridge: Marie is killed in the film's first action sequence to motivate Bourne to come out of hiding.
- Sudden Sequel Death Syndrome: Marie, Danny Zorn and Ward Abbott.
- These Hands Have Killed: On the DVD commentary, Bourne's reaction after killing Jarda is described as a man that's fallen off the wagon.
- Train Escape: After Bourne is identified at a hotel.
- Trapped in a Sinking Car: Bourne's car goes careening off a pier due to the assassin that is trying to kill them. He escapes, but his girlfriend got fatally shot in the process.
- Villains Out Shopping: Kirril's seen hanging out at a Moscow nightclub (in the middle of the day!) when Gretkov calls him back, telling him that Bourne is still alive.
- The Worf Effect: Bourne is incredibly cautious when he faces Jarda, with good reason. He's a particularly brutal fighter.
- Yank the Dog's Chain: The death of Marie in the beginning of the film.