Ultimately the movie is very faithful to the plot of the novel, hitting most of the major plot elements. Its major changes are cuts due to time, including a major plotline involving ordinary citizens on the streets of Manhattan, extended sequences about the pasts of the superheroes, and the Black Freighter plotline which consists of a story being read from a comic book. There are a few notable omissions or restructures from the original story, including (list does not encompass minor scene trims or changes for pacing, merely major plot points):
-A minor change is the birth date of the Comedian: in the graphic novel he 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.
-A small but significantly notable change is that 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?" 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.
- It's now Dan Dreiberg, not Rorschach, who breaks the news of the Comedian's death to Adrian Veidt.
- The setup which gets Rorschach arrested is different. In the movie, Rorschach goes to Moloch (Matt Frewer)'s apartment after doing research on Roy Chess (Douglas Chapman), the man who attempted to assassinate Adrian Veidt. At Chess's apartment, Rorschach found Chess's 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 to pieces with a butcher knife; 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 omission of the background story of Rorshach's psychiatrist. In the novel we see how the psychiatrist's home life and emotional equilibrium is wrecked by his intimate contact with Rorshach, 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 Rorshach.
- Rorschach's second costume, and the confrontation with his landlady. Whilst the comic mentions Rorschach's landlady many times, including having a TV interview with her when he's captured, 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 theatrical cut has Rorschach simply retrieving his old costume from Dr. Long during the prison riot, and Snyder has made reference to this being a cut he somewhat regretted, which also does not appear in the Director's Cut.
- The death of Hollis Mason. It has definitely been confirmed that this has been shot (footage of this scene does appear in the Japanese trailer), and appears, along with several additional scenes of Mason, in the Director's Cut.
-Tales of the Black Freighter. In the graphic novel, there is a second narrative weaved into the main one in the form of a pirate comic a young boy is reading on a New York street corner. The plot is allegorical to Veidt's quest to stop the coming war: a shipwrecked man, believing pirates are headed to his home town, undertakes a grueling journey to reach his home and sound a warning, committing increasingly horrific acts as desperation drives him. He ultimately discovers that the pirates never went to his home after all, and deciding that "I was a horror; amongst horrors must I dwell," he consigns himself to join the Black Freighter's crew. This is significant in that the story reaches the opposite conclusion as Veidt, who stops just short of telling Dr. Manhattan that he dreams of swimming towards the pirate freighter, indicating his deep-seated worry that his actions may have been unjustifiable.
An extended cut of the DVD will interpolate an animated version of this story, which is slated for a holiday 2009 release. Rumor has it that Alan Moore put the Tales of the Black Freighter in to represent his own personal struggle with DC comics.
- The finale. Instead of a genetically-engineered squid-like life-form passing off as an alien landing in the heart of New York, Veidt instead releases 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 loses it at an unconcerned Veidt, who merely tells him "a world at peace, Daniel. There had to be sacrifice."