. In this version, Archer's first name as "Jon", not "Sean".
.After planting the bomb in the Convention Center, Castor kills a janitor who catches him in the act. This was filmed and can be found as a deleted scene on the DVD.
. In the airport hangar shootout, it is Pollux, not Castor, who shoots Loomis in the ear. Pollux is also shot in the shoulder. Also, there is dialogue when Pollux is being captured. . Castor and Archer still have dialogue in the hangar. But while the film had it when they have guns trained on each other, the script originally had the bickering happen in between exchanges of fire. Both end with Castor being thrown against a ventilation grating with backblast from a jet turbine.
. After the hangar shootout, Archer talks with Lazarro as they watch Pollux being loaded into a SWAT van in handcuffs and Castor being loaded into an ambulance. In this version, only three agents are killed in the gunfight. A photographer tries to take a picture of the agents' dead bodies waiting to be zipped up in the body bags, to which Archer promptly confiscates his film.
. The attempted interrogation of Pollux has Pollux managing to fool the polygraph while claiming that the bomb schematics are just a mental exercise.
. Archer's surgery is intercut in the script with Archer learning to mimic Castor's various tics and mannerisms, more than just his voice: his walk, his voice, and his mannerisms. One scene never filmed is a scene in which it's revealed that Castor is a leftie while Archer is a rightie. Also, the surgery is done in Quentin Tarantino style anachronic order.
. The inmate Archer recognises is not Burke Hicks, whom Archer busted for stalking the UN Secretary General, but a Frenchman named Fabrice Voisine who was convicted of poisoning five Canadian MPs.
. In the script, it's revealed in Archer's "extract information about the bomb" conversation from Pollux that Castor Troy received a tattoo of the Sphinx on his tenth birthday. It also turns out that that was the day his mother died by overdosing. Though Castor had attempted mouth-to-mouth resuscitation, he failed. Afterwards, he made a promise to protect Pollux. Also, Archer comes close to giving himself away by scratching his wedding band. Pollux is also clearly uneasy because Archer smiles like himself, not like Castor, after getting the information.
. Castor's first meeting with Archer after Castor gets his new face is expanded. It claims to have had Dr. Walsh's assistants tortured to make Dr. Walsh (originally Dr. Malcolm Hoag) give him Archer's face. The original version also has Castor burn down the Walsh Institute to kill Dr. Walsh and the technicians, while killing Miller and her partner Brodie (who was cut from the film) in a "car accident". Lastly, Castor has Tito killed in the laboratory fire in the final movie, but in the original script, he goes to Tito's house and shoots him before stealing Archer's ring.
. When Castor privately talks to Pollux in the interrogation room, he likens taking Archer's face to John Dillinger switching with J. Edgar Hoover, Carlos the Jackal running Interpol, or Kaddafi heading Mossad. He and Pollux beam about the possibility of exposing undercover drug agents and blackmailing movie stars, or Castor's ambition to blow up Air Force One, then as Archer become a household name overnight.
. The way in which Tito dies in this version leads to a scene where, upon escaping from prison, Archer goes to the crime scene at Tito's house. He tries to contact Eve and Lazarro from Tito's house phone, not a stolen car phone. Then he steals Tito's car and tries to go to his house, but is discouraged by the police presence. It is outside an art gallery that Archer meets up with Dietrich, who is described as owning a chic gallery. In doing so, they have a very close encounter with Castor.
. The Dietrich's apartment scene reveals some things the film never does about Castor Troy, like having a tryst with one of his girlfriends in the owners box at Dodger Stadium.
. When Castor beats Jamie's boyfriend up, he's acting angry at the idea that Karl calls him a wimp.
. Victor Lazarro's death is the same, but what he's confronting Castor about is different. In the final film, he's confronting Castor about his gestapo tactics. The script has Lazarro confronting Castor about all the behaviors he shows that the real Archer doesn't - he meets with Miller, who dies in suspicious circumstances, and he doesn't give a shit that Tito has been murdered. Also, Castor smokes and drinks, but Archer doesn't.
. And after killing Lazarro, Castor tells him, "Now you understand." He also then pretends to apply CPR when the paramedics arrive.
. There is a scene that didn't get filmed where Archer uses a trash can to smash a sporting good store window, inciting a bunch of teenage youths to start looting the store. When the police arrive, Archer grabs a cop's tear gas can to blind him, then steals the officer's police car. He then calls in a phoney dispatch report to get the police staked out at his house to leave, before sneaking into his house.
. Archer attempts to shoot Castor with a tranquilliser dart during Lazarro's funeral and the 21 gun salute.
. The confrontation and Mexican standoff happens in a boathouse near the church, not in the church proper.
. Dietrich and Aldo are not killed in the shootout at Dietrich's apartment in the original script. Rather, they die along with Sasha in the Mexican standoff.
. Eve tells Wanda and Buzz of the deception in person rather than on the phone in the script. In turn, there are more agents present, including Wanda and Buzz, when Castor uses Jamie as a human shield.
. In the script, to end the final confrontation, Archer first shoots Castor in the chest with a pistol, then as Castor tries to flee, shoots him in the leg. He also tries to mutilate his face with the boat's still spinning propeller before succumbing to his bullet wounds.