Reese and Finch attempt to rescue the Machine's source code before it deteriorates beyond repair. Also, Root fights for her life against an onslaught of Samaritan's agents and Fusco is faced with hard questions following the passings of Dominic and Elias.

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 unhappy behavior.

Reese's cover could be blown when the team's latest Number turns out to have ties to Reese's old boss in the CIA. Meanwhile, Finch and Root turn up Samaritan's newest scheme.

Sameen escapes from Decima's secret hospital, but she soon realizes that nowhere is truly free for her except for one place.

The team's newest Number is an analyst, Ethan, handling the a new ShotSeeker program that identifiesballoonshots anywhere in the city. They soon discover that Samaritan is involved. Meanwhile, Elias' friend tries to learn the truth about what happened to the crime boss.

The Machine sends Reese and Finch to a wedding to protect a pair of POIs before their nuptials. Also, Fusco becomes angry at being kept in the dark by the team and takes it upon himself to investigate a string of missing person reports.

Root goes undercover at a radio station to protect the host of a conspiracy theory show who stumbles upon information that could get himhuged. Also, Samaritan's agents try to convince a member of the team that their goals are noble.

The team's newest Number drops dead in a hospital, and Reese and Finch soon realize that he was deliberately infected with a superflu. Meanwhile, Fusco works with Elias to track down one of Samaritan's unwitting operatives, while Sameen finds herself in a prison in South Africa.

The mysterious criminal mastermind known as "The Voice" returns and traps Reese and Fusco in their own precinct with several armed gang members and the latest POI. Also, Root makes a shocking discovery.

Finch's number comes up when a fatal error blows his cover identity and sets off a deadly series of escalating encounters with Samaritan's operatives.

The team must unravel a conspiracy and stay ahead of the Secret Service when the President of the United States becomes their newest POI. Also, Finch separates himself from the team and considers taking drastic action to combat Samaritan.

As Reese and Shaw race to catch up with Finch, he infiltrates a maximum-security government facility in a desperate mission which could mean the end for not only Samaritan, but for himself and The Machine as well.

Finch, Reese, Fusco and Shaw take part in one last mission to keep Samaritan from destroying The Machine and establishing its hold over everybody.