The Machine identifies another gripping season's worth of potential crimes that must be stopped. Adversaries from Reese's undercover past and Finch's government work threaten the team's crime-fighting mission and anonymity. Meanwhile, Detectives Carter and Fusco face down FBI probes and the dangerous tentacles of the police conspiracy known as "HR".
With Finch missing - kidnapped by his hacker nemesis, Root, in last season's finale cliffhanger - Reese enlists Detectives Carter and Fusco to get his friend back.
Reese and Carter head to Bishop, Texas, to investigate the cold case of Hannah Frey, who disappeared after leaving a library 20 years ago. Reese is convinced that Hannah is actually Root and hopes to locate Finch by uncovering more about her past. Meanwhile, Root forces Finch to watch as she tortures Denton Weeks, hoping to uncover the location of the Machine. Finch manages to help Weeks free himself briefly, but Root quickly turns the tables and kills him after extracting the last bit of information from him. Reese and Carter follow the evidence in Texas and eventually discover that Hannah Frey was killed and her body was hidden in Texas, but her best friend Sam Groves later became Root. Using financial information they find during the case, Reese manages to track down Root's credit card transactions to the small town in Maryland where she's holding Finch. He hightails it to Maryland and manages to intercept them at a train station, where Root nearly kills Finch before fleeing the scene. Later, after Reese returns Finch to the safe confines of the library, Root calls to warn him that she will be back. Back in New York, Fusco is charged with taking care of Reese's new dog, Bear, and with continuing the investigation into the Alicia Corwin murder case. When he stumbles upon a break in the case and overhears Hersh talking about Weeks, he immediately informs Reese, who pieces it all together to find Finch.
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.
When The Machine gives them the number of a mob enforcer whose life becomes endangered, Reese and Finch must decide whether to intervene or allow karma to balance the scales of justice. Meanwhile, Finch seeks aid from an unlikely source.
Reese must protect an investigative journalist through surreptitious means to avoid becoming part of her story.
Reese goes undercover in an idyllic neighborhood when The Machine's latest number sends him to the suburbs.
The Machine gives Finch and Reese the number of a brilliant surgeon, but they soon discover that a resourceful third party has raised the stakes for this POI, forcing them to turn to an unlikely source for help.
The team is spread thin when a husband and wife's numbers both come up.
Finch and Reese's surveillance skills are pushed to the limit when a New York City cab driver's number comes up and any one of his passengers could be involved in the impending crime.
While the FBI refocuses their efforts to catch "The Man in the Suit," Reese's latest POI becomes a personal quest after he learns that she's the sister of a soldier who was killed in action.
Finch goes undercover as a high school substitute teacher to protect a teenage genius who reminds him of his own adolescence as a child prodigy, while Carter undertakes a dangerous mission to stop the FBI from discovering that an imprisoned Reese is the "Man in a Suit."
While Carter engages in mental warfare with the FBI to help Reese evade Agent Donnelly's narrowing focus, Reese crosses paths with foes both old and new. Meanwhile, Det. Fusco is forced to fly solo to help the team's newest POI: supermodel Karolina Kurkova.
Reese is abducted by an old acquaintance planning a massive act of cyber-warfare that could lead to Reese's death.
Reese and Finch meet their match in a tech billionaire POI whose curiosity and limitless resources threaten to expose their identities and sabotage their efforts to save his life.
Reese and Finch race to save a hotel maid's life but find themselves surrounded by more suspects than they may be able to eliminate when they realize any guest or staff member could be her potential killer. Meanwhile, Detective Carter weighs a major offer from the FBI.
Reese's counterpart, lethal and sexy government operative Samantha Shaw (guest star SARAH SHAHI), 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 ever when they discover that her remarkably elusive skills equal their own.
After the machine gives Reese and Finch six numbers at once, their search for clues leads them to a coastal town where they are forced to ride out a storm with a group of locals in a police station. However, as the weather rages outside, a sinister situation arises inside when they realize there is an unidentified killer hiding among them.
When an elderly card sharp's number comes up, Reese and Finch travel to Atlantic City to delve beneath the surface of their POI's seemingly ordinary life for answers. In New York, Carter's crusade to clear a fellow detective's name brings her perilously close to identifying the remaining HR faction within the department.
When the number of a leading tech executive comes up, Finch infiltrates her corporation to gather intel but can't determine whether she is working in her company's best interest or planning to destroy it from the inside. Meanwhile, Carter continues to question Detective Beecher's integrity after he provides incriminating information about a fellow detective.
When a luminary in the world of medicine is poisoned, Reese and Finch have just 24 hours to determine the deadly toxin he was given and find the person behind the attack. Meanwhile, Detective Fusco's past corruption catches up with him when an informant gives the Internal Affairs Bureau the crucial information they need to send him to prison.
Reese and Finch realize that a virus has rendered The Machine erratic, causing it to issue numbers irregularly. As they race against the viral countdown, the team searches for a tech millionaire so elusive no one has ever seen him. Also, Detective Carter's mission to bring Cal Beecher's murderer to justice lands her squarely within the sights of the HR criminal organization.
Reese & Finch team up with surprising allies in a race to save The Machine from Root and the mysterious international organization Decima, who have both re-emerged with dangerous agendas. As the POI team faces off against enemies old and new, the nature of Finch's relationship with former partner Nathan Ingram is revealed along with his original motivation for wanting to save The Machine's irrelevant numbers. Meanwhile, in her mission to bring Cal Beecher's murderer to justice, Detective Carter finds herself up against the criminal organization known as HR.