To give this movie its gritty, documentary-style appearance, director Paul Greengrass used mostly handheld cameras, and a muted color palette. Greengrass also made sure to avoid computer graphics at all costs, and all of the stunts shown in the movie were achieved practically.
In the house in Munich, when Jason Bourne uses the rolled newspaper as a weapon, the martial art he performs is derived from Escrima, an old Philippine martial art, also called Arnis or Kali. This fighting style mainly uses sticks to fight, and in modern times the use of everyday objects is taught, including ball pens (as seen in The Bourne Identity (2002)) and rolled up newspapers. In the film it is combined with Bruce Lee's Jeet Kune Do.
Regarding the famous use of a rolled-up magazine as a weapon, fight coordinator Jeff Imada explained, "I would go around the set after it had been dressed and get an idea of what would be lying around and how it could be used as a weapon. I came up with the idea of using a rolled up magazine and had to convince a few people that would actually be a functional weapon. I had to demonstrate it by rolling it up and hitting it on the table to show how hard the impact would be. And also Matt [Damon] and Marton [Csokas] verified that the magazine would actually hurt because they'd be hitting each other in the arm before takes and would actually get bruises from it."
Unlike The Bourne Identity (2002), screenwriter Tony Gilroy read the book this time and claimed that he did a re-imagination, not an adaptation, of the novel. Gilroy wrote an original screenplay using key events and characters from the novel as a framework, though he replaced the traditional Carlos The Jackal-type villain with Kirill.
Producer Frank Marshall selected Paul Greengrass as director after he'd seen Greengrass's Bloody Sunday (2002). Marshall was after a director who wasn't intrinsically associated with the action genre, feeling that Greengrass would impart an original spin of his own to the script.
When Bourne visits the assassin Jarda in Germany, it is never made clear how Jason knew where he was or even who he was. There is one section of dialogue exchanged as - Jarda: "Word in the ether was you'd lost your memory." Jason Bourne: "You still should have moved." - giving the only indication of remembrance. According to the script Jarda is actually the Driver in the Berlin Flashbacks Jason is having. Also, deleted dialogue between Jason and Jarda further explain that Jarda had found Bourne and Maria somewhere in Greece, but Bourne got a leg up on Jarda and could have killed him. In the script Jarda asks Bourne "Why didn't you kill me then?" in which Bourne replies "Because she didn't want me to.".
The address of the Hotel Becker, where Neski was killed, is shown to be Kurtürstendamm 288. This address no longer exists but was the historical location of the Romanisches Café, a meeting place for intellectuals in pre-war Berlin.
While Bourne goes to look for Neski at her old house, the Russian cab driver receives a call, presumably by the Moscow police who alert him of Bourne, but the cab driver answers in German even though the scene is supposed to be in Moscow, Russia.
In Berlin, after researching Pam Landy's hotel, Bourne drives past a demonstration against globalization by activist organization ATTAC. The posters on the wall behind the man with the flag on the sidewalk read "Die Welt ist keine Ware", which means "The world is not for sale".
In a 2012 BAFTA Screenwriters' Lecture, uncredited screenwriter Brian Helgeland explained that part of Tony Gilroy's initial script was set in the USSR, even though that government had fallen over 10 years earlier. Helgeland was brought on five days before production began and completely rewrote Gilroy's script. Although the studio rejected the new script, they did change the USSR setting. Throughout production, Paul Greengrass would change Gilroy's script with Helgeland's, resulting in the final film.
Bourne carries a SIG-Sauer P225 (the same model gun he takes from cops in The Bourne Identity (2002)). There is some confusion over the model of the gun because Bourne shoots 12 rounds through it without reloading and a real P225 only holds 8 rounds in the magazine plus one in the chamber. Kirill uses a P99 and Jarda a Beretta 92FS.
The trivia items below may give away important plot points.
The film was made with no intention of making a third movie after this one; the final scene was also meant to give the Bourne character some closure and properly end the series. When The Bourne Ultimatum (2007) was green-lit, the writers had to write the story around this epilogue.
The film originally ended with the confession to Neski's daughter. Following previews, which found the ending too bleak, the New York postscript scene with Bourne and Landy was shot, just weeks before the film's release in the summer of 2004.
It took 4 days to shoot the sequence where three assassins close in on a house they suspect harbors Bourne, but he has already left and rigged the house to explode. When it does, three stuntmen wearing cabled harnesses are violently yanked up and away from the explosion, landing on off-camera airbags. Six cameras simultaneously covered the brief sequence.
In a draft version of the script, Bourne passes out in Moscow after revealing all to Neski's daughter and wakes up in a hospital in Ramstein Air Base in Germany. Landy tells him his name is "David" and hands him a file with details about Treadstone and his own life. After leaving, a nurse takes food to Bourne but the room is empty. He has disappeared again.
Before Brian Helgeland did his rewrite, Tony Gilroy's initial draft of the screenplay was vastly different. Instead of Kirill shooting her, Marie dies by accident when a bus veers off the road and slams into her. Bourne is outraged and goes berserk on the driver, almost killing him until the police arrest him. A large section of the film is then spent in an Indian prison, where Bourne makes numerous allies and enemies before planning his escape. From then on in, both scripts follow a similar track.
The room where Ward Abbott stays in The Westin Grand hotel in Berlin is the Goethe Suite, one of several historical-themed and decorated suites in this hotel. Johann Wolfgang von Goethe was the playwright of the two-act tragedy 'Faust', about a deal with the devil. Abbott's stay in this suite is suitable, since in a way, he himself "made a deal with the devil."
After the Berlin part Bourne leaves for Moscow. Several scenes taking places in the Russian Capitol were still shot in Berlin, which you can see on certain buildings and some traffic signs. Two of those supposedly Russian locations are Berlin Frankfurter Allee and Alexanderplatz.
When Kirill is staging the explosives on the circuit breakers to frame Bourne, he is wearing these cool, black "Foot Joy" golf gloves, one for a right-handed golfer, the other for a left-handed golfer. The famous "FJ" label is on top of both gloves.