The game starts with PreCrime Captain John Anderton pursuing future murderer Andre Serena throughout a meat packing facility. Anderton bests Andre and fellow PreCrime officer Barry arrives to subject the latter to virtual reality (the preferred form of punishment).
Anderton arrives at PreCrime HQ in Washington, DC where he is greeted by FBI agents Danny Witwer, Ben Mosely, and Ken Nara. Witwer explains that he was sent by the Attorney General to overlook the operations of PreCrime. Barry alerts Anderton to a vision by the Precogs: John Anderton will be murdered by Nikki Jameson, a consultant of SOL Enterprises. Anderton, Barry, and Mosely arrive at SOL to apprehend her, but she escapes. Returning to HQ, the Precogs generate a new vision, revealing that he will murder Roy Verhagen, a man he had never met. Barry witnesses the vision and attempts to help John escape. As Anderton fights his way to escape PreCrime HQ, he confronts Mosely and soundly defeats him.
Anderton goes to the mall to find Rufus, a former criminal that runs a club. Back in his apartment, Barry informs him that the city has a bounty on him. He also tells Anderton that 2 out of the 3 Precogs have a report, with the last one's MIA, suspecting a glitch. Anderton has Barry send him info on Iris Hinemen, the woman who initiated the Precogs program. PreCrime officers arrive to arrest him, and he makes his way to the rooftops, where Witwer confronts him in a hovership.
As this happens, Verhagen talks with Nikki, revealed to be a contractor hired to kill Anderton. Anderton reaches the botanical gardens, and finds Iris in the greenhouse, where she tells Anderton that he has fallen upon a scenario known as a "minority report": The Precogs are never wrong with their visions, but, occasionally, disagree on the outcome. This is kept secret from PreCrime and the perpetrator, and erased from the system. Both Anderton and Iris agree that public knowledge of the minority report would shut PreCrime down. Iris instructs him to find the dissenting Precog and download the information needed to clear his name, at which point PreCrime arrives, and Anderton has to protect Iris and leave the gardens.
Anderton meets a black market doctor at the Pepper Hotel to change his eyes and bypass the city's optical scanners. After commotion occurs, Anderton leaves, witnessing a riot against PreCrime. He evades the riots, and runs into agent Nara, beating him in a shootout.
Anderton arrives at PreCrime HQ to find Barry, who reveals Verhagen is the leader of SOL Enterprises, a multimillion-dollar company specializing in robotics, and a major weapons dealer in the black market. Anderton frees Agatha, a Precog, and they make their way out of PreCrime HQ.
After some evasion, Anderton takes Agatha to Rufus, who decodes her visions, and tells him about Shinya Okawa, former employee of SOL. Agatha returns to PreCrime as Anderton goes to meet Okawa.
On a subway train a PreCrime officer notices Anderton. With help from civilians that fought against PreCrime, Anderton commandeers the subway train car and defeats Mosely again.
In the ruins of the Sprawl, Anderton sees ongoing riots. He finds Okawa inside his fortune cookie factory. After a heated discussion, Anderton retrieves Okawa's computer in exchange for Verhagen's location.
Anderton fights through a waste management facility which has a backdoor to Verhagen's lair. Nikki joins the fight; she is beaten by Anderton. Anderton pursues Verhagen as Witwer and two PreCrime officers arrive. As Verhagen attempts to escape, Anderton cuts him off and holds him at gunpoint. Verhagen begs for mercy, offering Anderton bribes, which he refuses, and a gunshot is heard as the screen fades to black. As it cuts back, Verhagen sees that Anderton deliberately missed the shot.
Anderton witnesses Verhagen's imprisonment firsthand. Content with the results, Anderton is reinstated into PreCrime.