Season 5

1. B.S.O.D.

In the aftermath of Samaritan's attack known as "The Correction," Fusco is being questioned by Internal Affairs and the FBI, who believe he shot Dominic and Elias. Reese and Finch return to the subway hideout, where Harold tries to repair the damage done to the piezoelectric battery charging the briefcase containing The Machine. To his surprise, it starts decompressing on its own, resulting in a fire. Flashbacks to 2006 show Harold apprehensive about the Machine's ever-expanding capabilities, leading him to erase the Machine's memories every night at midnight. Once Root escapes Samaritan's operatives, she seeks refuge in the hideout of one of her former hacker/assassin associates, but he sells her out.

Reese joins her to battle a team of Samaritan operatives. They steal 300 PlayStation 3s to create enough storage for the Machine. Harold downloads the Machine, while Reese keeps the systems from overheating with liquid nitrogen. When Finch asks the Machine, "Can you see me?", after a few seconds go by, it responds by opening an empty command prompt followed by a long string of code showing its reboot.

2. SNAFU

Finch decides to use Reese and Fusco to run a surveillance test. Following malfunctions in the facial recognition system, Reese and Finch steal 64 next-generation GPU blade servers which, once connected to the networked PlayStation 3s, are used to reboot the Machine at full power. When the Machine shows signs that it's failing to place threats in context, Root and Finch have it run a contextual background on them, leading to it identifying them as threats and locking them out of the system. The Machine has lost the ability to differentiate between past and present, forced to relive the 42 times Finch killed it.

Reese engages in a firefight against an amateur assassin the Machine sent after him. Root puts herself under an anaesthetic so the Machine cannot use her cochlear implant against her and Finch has to convince the Machine that the team are not threats. Upon the Machine's first reboot, it provided 30 different numbers, most of whom were not involved in violent crimes; however, one of those numbers, ex-con Jeff Blackwell ( Josh Close ), was dismissed as someone who was not involved in any nefarious activity, only to be recruited by Samaritan.

3. Truth Be Told

In flashbacks to 2010, Reese and his partner Kara Stanton from the CIA are told to investigate a soldier and kill him after confirming that he sold information to the Taliban. In present day, The Machine gives the number of Alex Duncan ( Stephen Plunkett ), who turns out to be the brother of that soldier and who has found himself in trouble with the CIA through investigating his brother's death, since doing so could expose an off-book operation. Reese rescues Duncan from his old boss, Terrance Beale ( Keith David ), the very same agent who sent Reese and Kara to kill Duncan's brother, and they both lie to Duncan about his brother's ignominious death.

Reese leaves on good terms with Beale, who agrees to keep Reese's existence a secret. Meanwhile, Finch and Root investigate malware that Samaritan has been using to infect the firmware of electronic devices. Root runs the malware on an airgapped laptop disconnected from any external sources. Reese decides he can no longer see Dr. Iris Campbell for the time being, claiming that he is unable to lead a "normal life," after which he receives another number from Finch.

4. 6,741

Shaw is seen undergoing surgery by Samaritan operatives to have an electronic microchip implanted between her ear and her brain stem. She is able to turn the tables on them by breaking out of confinement and finding the team. Together, they trick Samaritan's operatives and capture Greer. With Greer in captivity, Shaw removes a USB drive embedded inside his arm which Finch is able to analyze, discovering it to be a kill-switch for Samaritan. Shaw had revealed to Root that she was subjected to extreme psychological torture while captive; once Greer starts to taunt her about the kill-switch and her mental state, she hallucinates heavily, loses control of reality, and kills him.

Shaw continues into a neurological downward spiral, causing her to kill Reese. She is about to kill Root when she confesses that Root was her only mental safe-place and turns the gun on herself. The narrative returns to the operating room and it is revealed that these events happened only in Shaw's mind. She has been subjected to thousands of electrochemical simulations by Samaritan so its operatives could see if she would lead them to the Machine and its assets. This particular simulation was number 6,741.

5. ShotSeeker

Reese protects an NYPD analyst named Ethan Garvin who works with an acoustic surveillance system called "ShotSeeker", designed to detect gunshots anywhere in the city. Samaritan had Ethan's friend Krupa killed because of her research and tries to cover up her murder and the existence of her work, by hacking ShotSeeker to engineer Garvin's death via suicide by cop and having Krupa's classmate and possible owner of her research files killed. Elias' associate and childhood friend, Bruce Moran ( James LeGros ) approaches Fusco to learn who killed Elias. Root meets Jeff Blackwell and tries to open his eyes about the true nature of his new employer.

Fusco has investigated so much about Garvin and Krupa that Samaritan labels him a "potential obstructionist." Root and Finch decide to make Krupa's research public to render Garvin irrelevant to Samaritan. The team reveal to Bruce that Elias is still alive, who encourages Bruce to go back to the shadows and embrace them. Finch and Root engineer a series of simulations in a Faraday cage between a small clone of the Machine and that of Samaritan, but every outcome is in favor of Samaritan with tens of billions of victories.

6. A More Perfect Union

The latest number belong to a marriage license, sending Reese and Finch to a wedding to prevent what appears to be a typical case of disapproval of the Groom by the Bride's father, however the situation proves to be more complex. Samaritan has now begun to track Fusco, having previously labeled him a "potential obstructionist". Root assigns the Machine's next number to Fusco. In an act of desperation, Greer takes Shaw on a "field trip", trying to bend her moral compass in favor of Samaritan. Fusco's investigation leads him back to Bruce Moran, who seems to be caught up in a Samaritan-engineered interference with a demolition project.

In another attempt to persuade Shaw, she is led to meet Gabriel, Samaritan's analog interface, who gives an apocalyptic depiction of what Samaritan is capable of. As the narrative returns to the biometric simulation room, revealing the events not to have been a simulation, but a manipulation of Shaw's thoughts and neurological activity. Fusco and Bear arrive at the eventual demolition site, finding many of the missing persons he has been investigating, including Krupa and a dead Bruce Moran, only to be caught in the middle of the demolition operation itself.

7. QSO

Root visits a recovering Fusco and hands him an exit strategy for himself and his son consisting of IDs and documents made by the Machine. The Machine discovers that Samaritan uses the radio wave frequencies of station AM 520 to communicate with its operatives via a sophisticated code that most people believe to be feedback noise. Upon realizing the reason why the Machine sent her there, Root uses Samaritan's own equipment to send a message to Shaw to give her hope. Finch does not necessarily agree with the Machine not forcing the radio host to quit, but Root believes the Machine allows for humans' free will and will not interfere with it.

After Fusco is recovered, he is visited by Finch who refuses to waver from his stance that keeping Fusco in the dark keeps him safe. Fusco points out that it is not working, and quits. Shaw is escorted by Lambert and told to kill an innocent woman. Believing that it is another simulation, Shaw complies and is later shocked when told that it was not a simulation. Shaw is about to kill herself when she receives the message from Root, regaining hope. She stealthily makes preparations to escape.

8. Reassortment

Reese and Finch become trapped in a hospital manipulated electronically by Samaritan to have initiated an outbreak of what it said to be a combination of H5N1 (avian flu) and live human flu virus; a synthesized, super-powered strain of the flu, and send Jeff Blackwell at the hospital. It appeared as though the epidemic was overkill to eliminate three targets in the hospital. Since the Machine is an open system, Root was able to use its abilities to find and retrieve a cure, saving the lives of two hospital workers and Fusco.

Shaw executes her escape plan and finds herself in a jail in Johannesburg, South Africa. While escaping, Lambert taunts her by claiming that she is actually in another simulation; she kills him, and is last seen driving in Lambert's vehicle at night at high speed, presumably to an airport. Fusco indefinitely chooses to distance himself from the team. Blackwell and his handler, Mona, discuss the quelled epidemic and declare it a success: The CDC is requiring everyone to be vaccinated, which will result in Samaritan learning everyone's DNA.

9. Sotto Voce

"The Voice", a criminal from the past has resurfaced and Finch turns to Elias for assistance. It is discovered that he has tracked Reese and Finch since their previous encounter in 2014. After a planned prison break of the "Templarios" gang, Reese and Fusco become trapped in the precinct against multiple enemies. Elias and Finch extract valuable information from an explosives associate. It is determined that "The Voice" is Terry Easton ( Neal Huff ), their number from the start. Finch finally meets him on the street, abhorring his devious acts. Elias stops him from killing Finch; as he drives away, Elias kills him remotely with a car bomb.

Meanwhile, Shaw finds her way back to New York and is reunited with Root. Root is overjoyed that Shaw is back, but Shaw, afraid of risking Root's life, threatens to shoot herself, simulation or not. Root threatens suicide as well, declaring that, if Shaw dies, they both die; Shaw withdraws. Reese and Finch decide to explain The Machine and Samaritan to Fusco. The three meet along the East River near the Queensboro Bridge. Joined by Root and Shaw, the Team is brought back together.

10. The Day the World Went Away

Finch's number comes up when his cover identity is compromised, due to a subconscious error, and Samaritan initiates a continuous dispatch of operatives on him. The team splits up in their escape, which results in Elias being killed by Samaritan agents while protecting Finch. The team rescues Finch from his potential capture and Root explains in the car her current understanding of herself and everyone else to be "information" that can never truly disappear, despite their deaths. Root is shot by Samaritan operative Jeff Blackwell and placed in critical condition while the police apprehend Finch, who is accused of treason.

A devastated Finch provides a soliloquy on how he intends to abandon the principles he has long followed and vows to kill Samaritan. The Machine calls Finch in the precinct, having taken on the voice of Root, who has died from her injuries. The Machine sets every criminal in the precinct free to allow Finch to escape; Reese and Shaw realize that Finch's number came up not just because he was a victim, but also because he's a perpetrator against Greer and Samaritan.

11. Synecdoche

Reese and Fusco reunite with Shaw after burying Root and travel to Washington, D.C. to protect their newest number, The President of the United States. But Shaw is worried about the implications behind Samaritan's neglecting to intervene. The threat is identified as a domestic terrorist group who are against the President's surveillance programs. The attempted assassination is stopped with the unexpected assistance of former POIs Logan Pierce, Joey Durban, and Harper Rose who each camouflaged themselves into various useful covers. The three reveal that they now work for the Machine, having been given the irrelevant number of Reese's cover identity while the team got the relevant number of the President.

Fusco, Shaw, Reese, Logan, Joey, and Harper discuss their enlistment by the Machine, what has happened, and what is to come before Logan provides the team with their next number: Harold. Harold, meanwhile, is grieving over the loss of Root and reaches a conclusion that brings him to a highly-secured government facility in San Antonio, Texas with a weaponized virus capable of destroying Samaritan, but with significant collateral damage. Harold has become ready to go to any lengths and Reese and Shaw prepare for their final battle.

12..exe

Fusco discovers that the missing persons he found in the tunnel as corpses have been discovered by the police and is kidnapped by Agent LeRoux, who reveals himself to be the killer. As Finch prepares to deploy his stolen computer virus (named ice-9.exe), he's hesitant because it will also destroy the Machine, so the Machine shows him a series of simulations of what would have occurred to each of the team's members if the Machine had never existed. Reese and Shaw are given a new number: one of John Greer's aliases along with coordinates to Fort Meade, where Finch has infiltrated the NSA and uploaded his virus onto the NSA's Intranet but is captured before he can activate it.

Greer tells Finch Samaritan's wish to rule the world together with the Machine. When Finch refuses to join, Greer sacrifices himself in an attempt to kill Finch by having all the oxygen removed from the room. Reese and Shaw infiltrate the building and activate a wireless modem to give the Machine access within, allowing it to save Finch's life. Finch confronts Samaritan and, with the Machine's encouragement, activates the virus.

13. return 0

The Ice-9 virus begins to have disastrous effects globally. Samaritan has uploaded a copy of itself to servers in the Federal Reserve. Reese and Finch infect Samaritan's servers there with the virus, but Samaritan uploads a compressed version of itself to a satellite. The Machine tells Finch that the only way to defeat Samaritan is to upload a copy of the Machine to the satellite and that whatever building he uses for the upload will be destroyed by a cruise missile. At the subway, Fusco and Shaw are attacked by Samaritan agents led by Blackwell.

They escape on the Machine's train, capturing Blackwell. Blackwell stabs Fusco and escapes. Finch realizes he's on the wrong rooftop, having been tricked by Reese and the Machine. Reese tells Finch he plans to sacrifice himself, as saving one life can make a real difference depending on the person. A grieving Finch leaves as Reese holds off Samaritan agents. A week later, the world recovers from the virus and Shaw kills Blackwell to avenge Root. She meets with a recovering Fusco as the Machine's copy returns to Earth before contacting Shaw, while Finch returns to his former fiancée, Grace.