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John Reese, a formerSpecial Forcessoldier andCIA operative, is burnt out andpresumed dead, living as avagrantinNew York City. He is approached byHarold Finch, a reclusive billionairesoftwaregenius who built a computer system for the U.S. government afterSeptember 11, 2001called the Machine, which monitorsall electronic communications and surveillance video feeds, in order to predict future terrorist activities. Finch and Reese attempt to understand the threat to, or by, people the Machine identifies as being under threat by providing only their social security numbers, and try to stop the crime from occurring. They are helped byNYPDDetectives Lionel Fusco, a formerly-corrupt officer whom Reese coerces into helping them, and Joss Carter, who initially investigates Reese for hisvigilanteactivities.
During the second season, Decima Technologies, a powerful and secretive private intelligence firm run by ex-MI6spy John Greer, is revealed to be attempting to gain access to the Machine. Carter vows vengeance against HR, a criminal organization within the NYPD, after they have her boyfriend, Detective Cal Beecher, murdered. Reese and Finch encounter Sameen Shaw, aU.S. ArmyISAassassin, on the run after being betrayed by her employers. The Machine is revealed to have developedsentienceand covertly arranged for itself to be moved to an undisclosed location to protect itself from interference.
In the third season, the Machine's sentience is fully revealed as it increasingly communicates with and proactively assists and directs the actions of the team. After being demoted due to HR's machinations, Carter brings down the entire organization, but is killed by its rogue second-in-command. The team also battles Vigilance, a violent anti-government organization devoted to securing people's privacy. A more advanced artificial intelligence called Samaritan is revealed. Samaritan differs from the Machine in being open to external direction and willing to remove those seen as disruptive to law and order pre-emptively.
Season Four covers the team's life in hiding. They continue to work on cases, but must now also evade Samaritan, which is seeking to resolve perceived problems of human violence by reshaping society, sometimes violently. Samaritan and the Machine meet via human proxies as the only two of their kind, and discuss their essential differences, disagreeing strongly on whether freewill or firm guidance is more beneficial to humanity. They part with the understanding that Samaritan will seek to destroy the Machine.
In season five, Finch steals and weaponizes Ice-9, a virulentcomputer viruscapable of infecting and destroying Samaritan, although it will also destroy the Machine and much of the global computing infrastructure as well. Greer sacrifices himself in vain to kill Finch and ensure Samaritan's continuation. The Machine ceases to function after showing Finch its prediction of the world and his friends' futures if it had not existed. Finch survives and reunites with his former fiancée. A while later, Shaw is unexpectedly contacted by the Machine; it has restored itself from the satellite to continue its work.