Forced to take on new identities provided by Root, the team members try to adapt to their new lives. However, some find it hard to ignore The Machine's numbers, which puts them all at risk of being detected by Samaritan.

While Reese is forced to go to counseling for his violent tendencies, Root, Shaw and Finch try to help a new POI.

Reese volunteers as an NYPD police academy instructor in order to keep an eye on a talented young officer whose suspicious actions make him question her motives. Meanwhile, Martine – armed with information from Samaritan – hunts a member of the team.

Reese must save Elias from the Brotherhood. He can't get any help from Root or Shaw since Shaw's cover is blown and Root is escorting her to underground.

Samaritan shows its power by erasing crime from the city for a day in an attempt to force The Machine out of hiding.

Samaritan launches a cyber-attack on the stock exchange, forcing the team to risk their lives in a desperate mission to stop a global economic catastrophe.

Reese and Finch scramble to protect a software CEO when his behavior becomes increasingly erratic following a hacker attack that reveals all his secrets and unravels his life.

Reese and Fusco get caught in the war between the two newest POIs, rival crime bosses Elias and Dominic. Also, a tantalizing clue to Shaw’s whereabouts leads Finch and Root into a possible trap, and Control goes rogue to uncover the true intentions of the Samaritan program.

The Machine experiences a glitch during rebooting, supplying Reese and Fusco with the numbers of dozens of people not actually involved in crimes, while also locking Finch and Root out after identifying them as threats based on past violent behavior.