Two years after the events of the first film, Jason Bourne and Marie Kreutz are now in Goa, India. Still experiencing flashbacks about his former life as a CIA assassin, he records them in a notebook.
In Berlin, two CIA agents subordinate to Deputy Director Pamela Landy are paying US$3 million for the "Neski files", documents on the theft of $20 million in allocation money seven years prior. The deal is interrupted by Kirill, an agent for Russia's Federal Security Service who works for Russian oil oligarch Yuri Gretkov. Kirill plants Bourne's fingerprint at the scene, interrupts the deal, kills everyone involved and steals the files and money. He travels to Goa to kill Bourne, but Bourne spots him and flees with Marie. Kirill shoots and kills Marie instead of Bourne. Their vehicle plunges into a river and Bourne leaves after unsuccessfully attempting to revive Marie.
Bourne travels to Naples, Italy with money and passports. After finding Bourne's fingerprint that Kirill planted, Landy asks Deputy Director Ward Abbott about Operation Treadstone, the defunct CIA program to which Bourne belonged. She tells Abbott that the CIA agent who stole the $20 million was named in the Neski files. Some years previously, Russian politician Vladimir Neski was about to identify the thief when he was supposedly murdered by his wife in a murder-suicide in a Berlin hotel. Landy believes that Bourne and Treadstone's late supervisor, Alexander Conklin, were somehow involved and that Bourne killed her two agents. Both Abbott and Landy go to Berlin to capture Bourne.
In Naples, Bourne allows himself to be identified by security. He subdues his CIA interrogator and copies the SIM card from his cell phone. From the subsequent phone call, he learns about Landy and the frameup. Bourne goes to Munich to visit Jarda, the only other remaining Treadstone operative. Jarda informs Bourne that Treadstone was shut down after Conklin's death, and tries to incapacitate him. Bourne kills Jarda and escapes before the CIA arrives. Bourne follows Landy and Abbott as they meet former Treadstone support technician Nicky Parsons to question her about Bourne. Believing that the CIA is hunting him again, Bourne calls Landy from a nearby roof and is told of the reason for his pursuit. He demands a meet-up with Nicky and indicates to Landy that he can see her in the office, shocking the entire CIA team.
Bourne kidnaps Nicky at the meet-up in Alexanderplatz, and learns from her that Abbott was the head of Treadstone, not Conklin. He remembers that he murdered Neski in Berlin, but Nicky knows nothing about it, so he lets her go. Bourne then visits the hotel where the killing took place and recalls more of his mission—he killed Neski on Conklin's orders, and when Neski's wife showed up, he shot her to make it look like a murder–suicide.
Danny Zorn (Conklin's assistant) suspects that Bourne was not involved. He explains his theory to Abbott, who kills him. Bourne breaks into Abbott's hotel room and records a conversation between him and Gretkov that incriminates them in the theft of the $20 million. Abbott admits to Bourne that he stole the money, ordered Bourne to murder Neski, ordered Kirill to retrieve the files, and have Bourne framed and silenced in Goa. Abbott expects Bourne to kill him, but Bourne, thinking of Marie, refuses, leaving his gun on the table. After Bourne leaves, Landy confronts Abbott about her suspicions and he commits suicide. Later, Landy returns to her hotel room where she finds an envelope that Bourne has delivered to her room containing the tape of Abbott's conversations with Gretkov and Bourne. Listening to the tape, she realizes that Bourne is now vindicated.
Bourne goes to Moscow to find Irena Neski, the daughter of Vladimir Neski. Kirill, tasked once again by Gretkov with killing Bourne, finds and wounds him. Bourne flees in a stolen taxi and Kirill chases him. After a long high-speed chase also involving police vehicles, Bourne forces Kirill's vehicle into a concrete divider. Bourne walks away, leaving a seriously wounded Kirill. Gretkov is subsequently arrested. Bourne locates Irena and confesses to murdering her parents; after apologizing, he leaves.
Later in New York, Bourne calls Landy; she thanks him for the tape, reveals to him his original name and date of birth, and asks him to meet her. Bourne then says, "Get some rest, Pam. You look tired", indicating that he is in New York and watching her.
There were no plans to make a sequel to The Bourne Identity (2002) when it was conceived. Matt Damon commented, "When The Bourne Identity came out I said, 'There is very little chance we will do a second film, just because nobody on the team who made the first wants to make another movie if it can't be as good as, or better than, the first one.'" According to producer Frank Marshall, the plot point of Marie's kidnapping to force Bourne back into his assassin persona in the novel The Bourne Supremacy and Bourne's threat to come after the CIA if they came after him again in the previous film, were the inspiration for the plot. Marshall said that screenwriter Tony Gilroy thought of an idea that Bourne "would go on what amounts to the samurai's journey, this journey of atonement." Producer Paul L. Sandberg felt that Gilroy's "veering away from the plot of the book" was necessary "because so much of the world has changed since the book's publication." The producers replaced director Doug Liman. This was mainly due to the difficulties Liman had with the studio when making the first film, and their unwillingness to work with him again. British director Paul Greengrass was selected to direct the film after the producers saw Bloody Sunday (2002), Greengrass' depiction of the Bloody Sunday shootings in Northern Ireland, at Gilroy's suggestion. Producer Patrick Crowley liked Greengrass' "sense of the camera as participatory viewer", a visual style Crowley thought would work well for The Bourne Supremacy. The film was shot in reverse order of its settings: some portions of the car chase and the film's ending were shot in Moscow, then most of the rest of the film was shot in and around Berlin, and the opening scenes in Goa were filmed last.
According to a June 2008 article from The Guardian, "Two weeks before [the film's] release, [Greengrass] got together with its star, Matt Damon, came up with a new ending and phoned the producers saying the new idea was way better. And it would cost $200,000 and involve pulling Damon from the set of Ocean's 12 for a re-shoot. Reluctantly the producers agreed—the movie tested 10 points higher with the new ending".
The Bourne Supremacy brought in over $52,521,865 on it's opening weekend, putting it at No. 1 for the weekend box office (July 23-25, 2004). The film went to gross over $176,241,941 (61.1%) in North America, with the international release being $112,258,276 (38.9%) resulting in a complete total of $288,500,217 worldwide.
The film received positive reviews from critics. Review aggregation website Rotten Tomatoes gives the film a score of 81% based on reviews from 189 critics, with an average score of 7.2/10. The site's consensus reads "A well-made sequel that delivers the thrills." At Metacritic, which assigns a normalised rating out of 100 based on individual reviews, the film achieved an average of 73 based on 39 reviews, indicating generally favorable reviews.
At the 2005 Taurus World Stunt Awards, veteran Russian stunt coordinator Viktor Ivanov and Scottish stunt driver Gillie McKenzie won the "Best Vehicle" award for their driving in the Moscow car chase scene. Dan Bradley, the film's second unit director won the overall award for stunt coordinator. The film ranks 454th on Empire magazine's 2008 list of the 500 greatest movies of all time.