The Machine, now completely self-governed with its whereabouts unknown, resumes giving Finch its "irrelevant" numbers for people in danger, which include a U.S. naval officer in town for Fleet Week. However, with so many sailors flooding the streets of New York City, finding the officer in time presents an even bigger challenge for Reese and Shaw.

The number comes up for an Internet entrepreneur in the business of eliminating people's privacy, but finds his own being rapidly stripped away. As his life spirals out of control, Reese tries to protect him while Finch calls on Shaw, Carter and Fusco for help finding whoever is after him.

When the Machine gives the number of Ian Murphy, a man suspected of being a stalker, Reese along with Shaw recruits Carter, Fusco and Zoe to investigate further into his background. But when they discover that Murphy has a son from a former lover who is now dead, they work to reunite the boy with his father and right the wrong set in motion by the boy's grandfather, who wanted Murphy dead after he didn't approve of him and saw him at his daughter's funeral. Meanwhile Root sets her escape plan in motion with the help of the Machine when government operative Hersh tracks her down. Finch arrives at the hospital and finds to his horror the hospital staff incapacitated and Root gone.

The team must figure out if a prominent lawyer orchestrated the murder of her husband or if she is being framed; Carter is spotted with Reese by her new partner.

Shaw must stay close to a 10-year-old girl with highly developed surveillance skills when she is identified by the machine; Carter's mission could be exposed.

After being freed from her confinement to the psych ward, Root needs Shaw's help with a directive from the machine; Finch and Reese look into a mild-mannered investigator.

The team is met with surprises during an investigation into a hypnotherapist; an antiquities dealer has ties to a crime organization.

The machine gives Finch 38 numbers at once; information about Carter's past is revealed.

The battle to bring a crime organization to justice reaches a new level; Reese's number comes up in the machine.

As the POI team seeks justice for Carter’s murder, Finch realizes one of his team members may go one step too far in order to end the war with HR. Also, The Machine gives out the number for NYPD Officer Patrick Simmons, one of the crime organization’s key players.

Flashbacks to Finch’s adolescence provide insight into his creation of The Machine. Also, the team receives the number of an already dying man, and Reese leaves the POI team behind in the aftermath of the war with the crime organization, HR.

Multiple enemies converge on the POI team as they protect a dying man whose number has come up. They struggle to keep their enemies at bay but without Reese, who has left them and their mission behind following the tragic war with HR, being down one man could have catastrophic repercussions for the team.

Reese boards an international flight in an attempt to put the team and the past behind him, but is angered when he realizes his travel plans have been manipulated.

Reese rejoins Finch in New York, but when the team receives the number of a highly skilled antiquities thief, a surprising turn of events finds them planning a heist which could land them all in jail.

Finch goes undercover in an emergency call center to protect a 911 operator, but it soon becomes clear that the threat reaches further than the team could have anticipated.

The secrets of Finch’s operation before he enlisted Reese are revealed, including shocking ties to present-day events.

The Machine assigns Root to seek out a janitor with a mysterious past, but when her very presence puts his life in danger, Finch also receives his number.

Finch and Reese must delve into the murky waters of international politics when they are given the number of a former government contractor who is stalking a UN diplomat. Also, an enemy attempts to gain an upper hand on Root.

Reese and Shaw pose as alumni at a high school reunion in order to keep eyes on the latest POI. Meanwhile, Finch and Fusco travel to Washington, D.C., to investigate the motivations behind Vigilance’s latest attack.

Reese poses as a Secret Service agent to get close to the latest POI, a U.S. congressman who may hold the key to derailing Decima’s plans to bring a second Machine online.

As Decima uses Samaritan’s feeds to hunt Reese and Shaw, Greer exploits Finch’s greatest weakness in an attempt to lure him out of hiding: his love for his former fiancée, Grace Hendricks.

When an unknown entity prevents The Machine from seeing the full picture of an impending catastrophic event, it sends the team five separate numbers to help them piece together the bigger picture. Meanwhile, Root’s team of hackers arrives in New York.