John Reese, former CIA paramilitary operative, is presumed dead and teams up with reclusive billionaire Finch to prevent violent crimes in New York City by initiating their own type of justice. With the special training that Reese has had in Covert Operations and Finch's genius software inventing mind, the two are a perfect match for the job that they have to complete. With the help of surveillance equipment, they work "outside the law" and get the right criminal behind bars.
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 deaths 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 violent behavior.
Reese’s cover could be blown when he realizes the latest POI has ties to his old CIA colleague, Kara Stanton.
Shaw escapes her captors, but the team is unsure of her mental state when she begins to act paranoid and reckless.
Reese protects an NYPD analyst whose investigation into a software glitch has drawn the attention of Samaritan. Also, Reese and Fusco are threatened by an ally of Elias’s, who is looking to avenge his friend’s death.
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 him killed. Also, Samaritan’s agents try to convince a member of the team that their goals are noble.
Reese and Finch become trapped in a hospital that becomes ground zero for a deadly viral outbreak. Also, Samaritan’s newest recruit has second thoughts and Shaw continues to struggle with reality.
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 embark on one last mission to prevent Samaritan from destroying The Machine and cementing its hold over mankind.