With Finch missing – kidnapped by his hacker nemesis, Root, Reese enlists Detectives Carter and Fusco to get his friend back, Meanwhile, The Machine never sleeps, disseminating a new number to Reese.

The Machine delivers the number of a cold case that leads Reese ever closer to catching up with Finch and his kidnapper, Root.

With Finch back in the Library, Reese returns to field work, only to face his toughest case yet – protecting the privileged daughter of a Brazilian diplomat.

Carter tries to help Reese by engaging in mental warfare with the FBI; Reese has encounters with old and new enemies; Detective Fusco must protect supermodel Karolina Kurkova, the latest person of interest.

As Reese and Finch try to save a hotel maid's life, they encounter a litany of suspects; Detective Carter considers a significant offer from the FBI.

A lethal government operative who tracks and stops terrorist threats before they occur finds herself on the run – and the new focus of Reese and Finch's attention. However, their pursuit proves to be their most formidable when they discover that her remarkable skill set equals their own.

Finch and Reese team up with unexpected allies as they race to fix the machine; as Detective Carter tries to apprehend Cal Beecher's murderer, she finds herself up against HR -- a criminal organization.

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.

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.

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.

The team takes desperate action in its race to prevent the malevolent AI program Samaritan from coming online and making them its first targets. Meanwhile, the months-long battle with the anti-surveillance terrorist group Vigilance comes to a shocking conclusion.