In April 2054, Washington, DC’s prototype PreCrime police department stops murderers before they act, reducing the murder rate to zero percent. Murders are predicted using specialized mutated humans, called “Precogs”, who “previsualize” crimes by receiving visions of the future. Would-be murderers are imprisoned in a benevolent virtual reality. The federal government is on the verge of adopting the controversial program nationwide.
Since the disappearance of his son Sean, PreCrime Captain John Anderton (Tom Cruise) has separated from his wife Lara (Kathryn Morris) and become a drug addict. While United States Department of Justice agent Danny Witwer (Colin Farrell) is auditing the program, the Precogs generate a new prediction, stating Anderton will murder a man he does not know named Leo Crow in 36 hours. Anderton flees the area as Witwer begins a manhunt. Anderton seeks the advice of Dr. Iris Hineman (Lois Smith), the creator of PreCrime technology. She reveals that sometimes one of the Precogs, usually Agatha (Samantha Morton), has a different vision than the other two; a “minority report” of a possible alternate future. This has been kept a secret as it would damage the system’s credibility. Anderton resolves to recover the minority report to prove his innocence.
Anderton goes to a black market doctor for a risky eye transplant to avoid the citywide optical recognition system. He returns to PreCrime and kidnaps Agatha, shutting down the system, as the Precogs operate as a group mind. Anderton takes Agatha to a hacker to extract the minority report of Leo Crow (Mike Binder), but none exists; instead, Agatha shows him an image of the murder of Ann Lively (Jessica Harper), a woman who was drowned by a hooded figure five years prior.
Anderton and Agatha go to Crow’s hotel room as the 36-hour time nears, finding numerous photos of children, including Sean’s. Crow arrives and Anderton prepares to kill him, accusing him of being a serial child killer. Agatha talks Anderton out of shooting Crow by telling him that he has the ability to choose his future now that he is aware of it. Crow, however, begs to be killed, having been hired by an unknown entity to plant the photos and be killed in exchange for his family’s financial well being. Crow grabs Anderton’s gun and pulls the trigger, killing himself. Anderton and Agatha flee to Lara’s house outside the city for refuge. There they learn Lively was Agatha’s drug-addicted mother who sold her to PreCrime. Lively had sobered up and attempted to reclaim Agatha, but was murdered. Anderton realizes he is being targeted for knowing about Lively’s existence and her connection to Agatha.
Witwer, studying Crow’s death, suspects Anderton is being framed. He examines the footage of Lively’s murder and finds there were two attempts on her life, the first having been stopped by PreCrime but the second, occurring seconds later, having succeeded. Witwer reports this to the director and founder of PreCrime, Lamar Burgess (Max von Sydow), but Burgess responds by killing Witwer using Anderton’s gun. With the Precogs still offline, the murder is not detected.
Lara calls Burgess to reveal that Anderton is with her, and he is captured, accused of both murders, and imprisoned after being fitted with the brain device that puts him into a dreamlike sleep. Agatha is reconnected to the PreCrime system. While attempting to comfort Lara, Burgess accidentally reveals himself as Lively’s murderer. Lara frees Anderton, who then exposes Burgess at a PreCrime celebratory banquet by playing the full video of Agatha’s vision of Burgess killing Lively. A new report is generated at PreCrime, indicating that Burgess will kill Anderton and in the process he will lose his life too. In a confrontation with Anderton, Burgess admits that PreCrime could not function without Agatha; he killed Lively following an actual attempt on her life that he had arranged, knowing that the murder would appear as an echo within PreCrime and be ignored. Anderton points out the dilemma Burgess now faces: he can kill Anderton and validate PreCrime at the cost of his own life, or he can spare Anderton and allow the program to be discredited and shut down. The flaw in the system, Anderton notes, is that people can change their future once they become aware of it. Burgess commits suicide.
Afterwards, the PreCrime system is shut down. All the prisoners are pardoned and released, although many remain under police surveillance for years. Anderton and Lara reconcile and prepare for the birth of a new child, and the Precogs are sent away to an undisclosed location to live their lives in peace.