The Theatrical Cut is more loosely based on the book than the Director's or Ultimate Cuts, while still being very close to the source material as it is. However, the Ultimate Cut is the most slavishly faithful, going so far as to include the "Tales of the Black Freighter" News stand subplot that took up a good portion of the comic book.
A few of the additions to the Director's (and, subsequently, Ultimate) Cut are actually scenes that were not in the graphic novel in the first place, most notably Rorschach's initial encounter with two cops at Blake's apartment. This scene, however, does not contradict any major plot points, and merely serves as character development.
A few other, minor changes include:
-The police investigation of Blake's murder & subsequent dialog between the two detectives that opens the 1st chapter of the graphic novel is reduced in favor of a scene depicting the fight between Blake and his attacker.
- In the graphic novel, The Comedian was born in 1924, but in the film he was born in 1918. This change was most likely done to accommodate the actor playing him, who simply could not be passed off as a teenager for the flashback to 1940 and without resorting to hiring another actor to play the younger Comedian.
- In the novel, the masked adventurers were never known as "The Watchmen." The name referred to the speech that JFK never got to make in Dallas (due to his assassination), which contained the line "We in this generation are by destiny, rather than by choice, the watchmen on the walls of world freedom." It also refers to the old Roman phrase "Who Watches The Watchmen?" a phrase that serves as the theme of the graphic novel and appears throughout it as unfinished graffiti. The proposed name for the second-generation costumed adventurers in the novel was "The Crimebusters," although the group never formed, and the name was never adopted.
- Dan Dreiberg, not Rorschach, breaks the news of the Comedian's death to Adrian Veidt. In the novel, Rorschach bypasses the security at Adrian's office by using his grappling gun to enter through a high window. Dan merely approaches Adrian as he's finishing up a press conference at his office.
- The setup which gets Rorschach arrested is different. In the movie, Rorschach goes to Moloch's (Matt Frewer) apartment after doing research on Roy Chess (Douglas Chapman), the man who attempted to assassinate Adrian Veidt. At Chess' apartment, Rorschach found Chess' ID card which showed he worked for Pyramid Transnational. Rorschach had seen this logo at Moloch's, and hence went to talk to Moloch and ended up being framed. In the book, Rorschach visits Moloch once more, before Veidt's assassination attempt. He tells Moloch to leave him a message in a trash can if he remembers anything that could help Rorschach with the mask-killer. Rorschach receives a note, and then arrives at Moloch's house to discuss the Comedian, when he is ambushed by the cops.
- Rorschach's hunting down of the kidnapper of Blair Roche. The movie keeps the majority of this sequence the same except for the death of the kidnapper. In the movie, Rorschach simply hacks the man's head to pieces with a meat cleaver; while in the novel, Rorschach gives the kidnapper a choice of cutting through his own arm that is cuffed to a wood stove or burning in the room Rorschach has set ablaze.
- The absence of the flashback sequence wherein an angry Laurie, having just learned (through Hollis Mason's book Under The Hood) that the Comedian tried to rape her mother, confronts him at Mason's honorary party. This scene is considered reasonably important by some as helping to establish Laurie's deep hatred of him, and why she spurns the knowledge that he's her father so strongly.
- The absence of the flashback sequence where Veidt invites Jon and Laurie to dinner at Karnak. This scene is important for being the introduction of the genetically-engineered lynx Bubastis, whose unexplained presence in the film has confused some.
- The subplot involving the two detectives who are assigned on to the Edward Blake case, which was a big part of the book. The two detectives are now only seen in two scenes.
- The omission of the background story of Rorschach's psychiatrist. In the novel we see how the psychiatrist's home life and emotional equilibrium is wrecked by his intimate contact with Rorschach, because "when you gaze into the abyss, the abyss also gazes into you." The Director's Cut adds some material to this scene, but does not depict scenes of the psychiatrist outside of his interview with Rorschach.
-A significant part of Rorschach's history, how he came to be Rorschach and how he discovered the material that makes up his "face" (mask), is omitted from the film. As Walter Kovacs he hears about the murder of a woman, Kitty Genovese, which moves him to become vigilante. Genovese was killed outside her apartment building. At the time the graphic novel was released it was believed that her neighbors did nothing to help her, analysis of the crime since then leaves that theory ambiguous. The movie does recreate the event that made him a sociopath, his investigation of the little girl's disappearance (see above).
- Rorschach's second costume, and the confrontation with his landlady. Whilst the comic mentions Rorschach's landlady several times, including having a TV interview with her when he's captured and her accusations of him trying to take advantage of her sexually, there's no mention of her in the film. As such, there's no scene of Rorschach retrieving his journal and spare costume, only to confront his stricken landlady. The film has Rorschach simply retrieving his old costume from Dr. Long during the prison riot.
-The scenes with Laurie on Mars with Dr. Manhattan deciding the fate of the world are intact except for a significant change: in the comic books, Laurie deduces through repressed memories that her mother had a romantic relationship with the Comedian despite his attempted rape of her years before. Laurie comes to this realization herself. In the film, Manhattan touches her head and releases the repressed memories she has.
- The finale. Instead of a genetically-engineered squid-like life-form passing off as an alien landing in the heart of New York in the novel, Veidt instead uses the "clean energy" sphere he'd developed with Manhattan to release a series of "energy bombs" (for lack of a better term) based on Dr. Manhattan's powers in cities around the globe, making Manhattan appear responsible. The consequences, the Watchmen's decision to take on a code of silence, and Rorschach's death all pretty much play out the same, though this time Nite Owl sees his death and yells in anguish. Dan also confronts an calm Veidt and beats him; Veidt does not resist or defend himself & merely tells him "a world at peace, Daniel. There had to be sacrifice."
- Unlike the book, the police never deduce that Daniel is Nite Owl, and neither he nor Laurie become wanted fugitives for breaking Rorschach out of prison. As such, they both stay in New York City with the apparent intention of resuming their superhero careers to some degree.
Several major scenes not included in the Theatrical Cut that are present in the Director's and Ultimate Cuts include the murder of Hollis Mason, along with Dan's furious outburst at the knot top in the bar, Dr. Manhattan's explanation of the symbol on his forehead, and Dan and Laurie having a conversation after they fight the knot tops in the alley. Mostly, however, the Director's and Ultimate Cuts make the film more faithful to the graphic novel not by adding lots of new scenes, but instead simply extending small pieces of dialogue here and there to expand on character development which was so prominent in the comics.