While Reese and Finch to get the Machine's deteriorating source code to the subway station so that they can restore it, Root deals with multiple waves of Decima agents trying to capture her and find the Machine's location.
The Machine ends up malfunctioning during a reboot and gives Reese and Fusco the Numbers of dozens of people not involved in any crimes. At the same time, it flags Finch, Root, and Reese as threats, and shuts Finch and Root out of the system.
Reese's cover could be blown when the team's latest Number turns out to have ties to Reese's old boss in the CIA. Meanwhile, Finch and Root turn up Samaritan's newest scheme.
Sameen escapes from Decima's secret hospital, but she soon realizes that nowhere is truly free for her except for one place.
The team's newest Number is an analyst, Ethan, handling the a new ShotSeeker program that identifies gunshots anywhere in the city. They soon discover that Samaritan is involved. Meanwhile, Elias' friend tries to learn the truth about what happened to the crime boss.
The team crash a wedding to protect a couple getting married. Meanwhile, Fusco continues his investigation into the missing persons, and Greer shows Sameen how Samaritan makes the world a better place.
The Machine sends Root to protect a radio host who has intercepted secret messages from Samaritan to its operatives... and to contact the captive Sameen.
The team's newest Number drops dead in a hospital, and Reese and Finch soon realize that he was deliberately infected with a superflu. Meanwhile, Fusco works with Elias to track down one of Samaritan's unwitting operatives, while Sameen finds herself in a prison in South Africa.
Finch's number comes up when a fatal error blows his cover identity and sets off a deadly series of escalating encounters with Samaritan's operatives.
The team must unravel a conspiracy and stay ahead of the Secret Service when the President of the United States becomes their newest POI. Also, Finch separates himself from the team and considers taking drastic action to combat Samaritan.