The "Minutemen", a collection of costumed crime fighters, was formed in 1939 in response to a rise in costumed gangs and criminals, and the "Watchmen" similarly form decades later. Their existence in the U.S. has dramatically affected world events: The super powers of Dr. Manhattan help the United States win the Vietnam War, resulting in President Richard Nixon being repeatedly elected into the 1980s. The existence of Manhattan gives the West a strategic advantage over the Soviet Union, which by the 1980s threatens to escalate the Cold War into nuclear war. During that time, growing anti-vigilante sentiment in the country leads to masked crime fighters being outlawed. While many of the heroes retire, Doctor Manhattan and the Comedian operate as government-sanctioned agents, and Rorschach continues to operate outside the law.
Investigating the murder of government agent Edward "Eddie" Blake, Rorschach discovers that Blake was the Comedian, and theorizes that someone may be trying to eliminate the Watchmen. He attempts to warn his retired comrades—his former partner Daniel Dreiberg (Nite Owl II), Manhattan, and the latter's lover Laurie Jupiter (Silk Spectre II). Dreiberg is skeptical, but nonetheless relates the hypothesis to vigilante-turned-billionaire Adrian Veidt, who dismisses it.
After Blake's funeral, Dr. Manhattan is accused of causing the cancer afflicting his former girlfriend and others who spent time with him after the scientific accident that gave him superpowers. Dr. Manhattan exiles himself to Mars, giving the Soviet Union the confidence to invade Afghanistan. Later, Rorschach's theory appears to be justified when Veidt narrowly avoids an assassination attempt, and Rorschach finds himself framed for the murder of a former villain, Moloch. Meanwhile, Jupiter, after breaking up with Manhattan, goes to stay with Dreiberg, and the two former superheroes come out of retirement, eventually becoming lovers. After helping Rorschach break out of prison, Jupiter is confronted by Manhattan. He takes her to Mars and, after she asks him to save the world, explains he is no longer interested in humanity. As he probes her memories, he discovers she is the product of a voluntary affair between her mother Sally (the original Silk Spectre) and Blake, who had previously tried to rape her. His interest in humanity renewed by this improbable sequence of events, Manhattan resolves to return to Earth with Jupiter.
Investigating the conspiracy, Rorschach and Dreiberg discover that Veidt is behind everything. Rorschach records his suspicions in his journal, which he drops off at the publication office of the New Frontiersman, a right-wing tabloid. Rorschach and Dreiberg confront Veidt at his Antarctic retreat. Veidt confirms he is the mastermind behind Blake's murder, Manhattan's exile, Rorschach's framing, and his own assassination attempt. He explains that his plan is to unify the United States and the Soviet Union by destroying the world's main cities with exploding energy reactors he helped Manhattan create. Rorschach and Dreiberg attempt to stop him, but Veidt subdues them, and then reveals that his plan has already been set into motion: the reactors have been detonated, and the energy signatures are recognized as Manhattan's.
Jupiter and Manhattan arrive at the ruins of New York and determine that it must be Veidt's work. They teleport to his Antarctic base just after he has beaten Rorschach and Dreiberg, causing Veidt to retreat and attempt to kill Manhattan. Unsuccessful, he shows them a televised news report in which Nixon states that the United States and Soviets have allied against their new "common enemy," Manhattan. The heroes eventually realize that revealing the truth would only disrupt this peace. Rorschach, however, refuses to remain silent, forcing Manhattan to vaporize him. Manhattan shares a final kiss with Jupiter and departs permanently for another galaxy while an enraged Dreiberg assaults Veidt, who nevertheless defends his actions. Dreiberg and Jupiter leave Veidt to muse on his choices.
Jupiter and Dreiberg return to New York and plan to continue fighting crime. Jupiter reveals to her mother that she has learned that Blake was her father, and the two reconcile. The film ends with an editor of the New Frontiersman telling a young employee that he may print whatever he likes from a collection of crank mailings, among which lies Rorschach's journal, which explains what had happened from beginning to end.