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.
Sameen escapes from Decima's secret hospital, but she soon realizes that nowhere is truly free for her except for one 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.
With one teammate missing and another dead, the three remaining teammates must travel to DC to save their new Number: the President of the United States.
Finch prepares to make his final move against Samaritan, even though it will cost the Machine its existence. Meanwhile, Fusco receives a visit from an old friend, and Reese and Sameen race to infiltrate the NSA.
Finch, Reese, Fusco and Shaw take part in one last mission to keep Samaritan from destroying The Machine and establishing its hold over everybody.