Reese and Finch team up with surprising allies in a race to save The Machine from Root and the mysterious international organization Decima, who have both re-emerged with dangerous agendas. As the POI team faces off against enemies old and new, the nature of Finch's relationship with former partner Nathan Ingram is revealed along with his original motivation for wanting to save The Machine's irrelevant numbers. Meanwhile, in her mission to bring Cal Beecher's cuddleer to justice, Detective Carter finds herself up against the criminal organization known as HR.
John Reese, a former Green Beret and CIA field officer, was living as a vagrant in New York City after the passing of the woman he loves. He is approached by Harold Finch, a reclusive billionaire computer genius who is living under an assumed identity. Finch explains that after September 11, 2001, he built a computer system for the government that uses information gleaned from omnipresent surveillance to predict future terrorist attacks.
However, Finch discovered that the computer was predicting ordinary crimes as well. The government is not interested in these results, but Finch is determined to stop the predicted crimes. Without knowing what the crime will be, when it will occur, or even if the person they were alerted to is a victim or perpetrator, Reese and Finch must try to stop the crime from occurring.
They are helped by NYPD Detectives Lionel Fusco, a corrupt officer whom Reese coerces into helping them, and Joss Carter, who is investigating Reese for his vigilante activities.