John Allison Anderton is the aging creator and head police commissioner of the Precrime Division, in which three mutant humans called "precogs" predict all crimes before they occur. While showing his new second-in-command Ed Witwer around the premises, Anderton is shocked to receive a report that he, Anderton, is predicted to murder a man within the coming week. Believing Witwer has framed him in order to steal his job, Anderton tells his much younger wife Lisa, who is a fellow police official. Becoming paranoid, he soon suspects that she and Witwer may be joined in a conspiracy against him.
Knowing that a copy of the report is automatically sent to the Army as a safeguard, Anderton rushes home. He is suddenly abducted and brought before Leopold Kaplan, a retired general and Anderton's expected murder victim, although the two have never met. Kaplan hears Anderton's claims of ignorance, but still moves to hand him over to police custody. However, a mysterious man named Fleming crashes Anderton's transport vehicle and, claiming that Anderton is being framed by Witwer, allows him to escape.
Anderton contacts a friend at Precrime to inquire about a "minority report": a type of dissenting opinion in which one of the three precogs' predictions conflicts with those of the other two. Indeed, he learns that a minority report exists: one of the precogs predicted that Anderton would refrain from murdering Kaplan once he became aware of the situation. Anderton must now decide whether to remain silent and turn himself in, or speak up about the minority report and thus reveal a flaw that could discredit the entire Precrime system.
Lisa confronts Anderton, claiming that no conspiracy is taking place. She attempts to help him escape using a police helicopter, but Fleming ambushes and attacks her. Anderton subdues Fleming, revealing that the latter is one of Kaplan's men. Anderton realizes that his escape and "framing" was staged by the military. By preventing Anderton from murdering Kaplan, while also preventing Anderton from being arrested, Kaplan hopes to destroy Precrime's credibility by showing that arrested "criminals" may not always become guilty of the crimes they are meant to commit. Anderton carefully listens to each of the precog reports, then goes to an Army rally where Kaplan is moments away from reading aloud Anderton's minority report to the public. Before he is able to do so, Anderton shoots and kills him.
Anderton is arrested and both he and Lisa, as his accomplice, are scheduled for penal transportation to another planet. Before they leave Earth, Anderton explains to Witwer his reasoning for shooting Kaplan. After obtaining the three precog reports, he discovered that each of them predicted a different outcome. He further realized that the reports had not been generated simultaneously, and that each had been affected by his knowledge of all preceding ones. The first indicated that he would kill Kaplan in order to prevent Precrime from being discredited and shut down; the second predicted that, after reading the first, he would decide to not kill Kaplan. According to the third report, Kaplan had planned to discredit Precrime in order to enact a state of emergency and martial law, resulting in a military coup in which the Army would replace Precrime. Wanting to preserve the status quo, Anderton decided to fulfill the prediction and assassinate Kaplan rather than letting his own innocence destroy the system he helped create. The entire situation thus became a self-fulfilling prophecy. As Anderton and Lisa are about to be transported, Anderton warns Witwer, who has nervously inherited Anderton's job, that the same predicament could happen to him at any time.
