Mr. Reese breaks Finch's code of communicating with the Machine in order to save the new number, Leon, who stole money from some Aryan outlaws. He then convinces the Machine to help him find Finch.
Detective Carter and Mr. Reese go to Texas to look into Root's past. Root shows to Finch that the people who bought his Machine are evil. Mr. Reese finally finds Finch.
Mr. Reese becomes the new bodyguard of the daughter of a Brazilian diplomat who parties with the wrong type of people. Finch finds it hard to readjust to society after his kidnapping.
The FBI are getting closer to the head of HR. Mr. Reese tries to prevent a young journalist that likes taking risks from being killed. To avoid getting media attention, Mr. Reese starts dating her. Fusco is playing double.
John and Zoe go deep undercover as husband and wife to get close to a person who's been using a dead guy's identity for the past 15 years. In a flashback Finch first meets Grace Hendricks.
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 and Carter are trying to get Reese out of Riker's, where he is still being kept prisoner by Donnelly. Meanwhile, Fusco is working alone on the next number.
Finch and Reese go undercover in a hotel to protect a cleaning woman who is the apparent target of Serbian killers. Meanwhile, Carter begins the process of joining the FBI and someone from their past unexpectedly returns.
The Machine suddenly provides six numbers, one of whom has a place on remote Owen Island. Because of a tropical storm Finch and Reese are trapped there with eight others, and one is them is methodically killing the others, one by one.
After saving Leon Tao yet again, Reese goes to Atlantic City to watch over a retiree who's losing a fortune in the casino. HR smears Szymanski so that he can't testify at a Russian mob trial and Carter risks her life trying to clear him.
Finch goes undercover at a tech company to watch a rising VP. The company appears to be riddled with agents who are a front for something more sinister. Shaw reappears and takes an interest in Root. HR decides to rub out an informant.
A respected doctor is poisoned with Polonium and has just 24 hours to help Reese find his killer. Carter, grieving over the death of Cal Beecher, helps Fusco when HR turns Internal Affairs against him.
They wait ten days for a new number due to a system virus, suspecting Root is the problem. It's for Ernest Thornhill, who isn't who, or what, he is supposed to be. At stake is The Machine - will it remain with Finch or end up with Decima?
Reese and 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.