Season 3

1. Liberty

Reese, Finch, and Shaw work to save the life of a sailor named Jack Salazar ( Rey Valentin ) who is inadvertently caught up in a diamond smuggling operation run by a team of Force Recon Marines. Shaw gets used to being a member of the team, although her propensity for violent solutions worries Finch. Meanwhile, Carter adapts to life as a uniformed police officer after being demoted. It is revealed she is conducting a secret investigation into HR, and has identified several of its high-ranking members. A troubled Root continues to receive counseling, and later reveals that she is still in contact with the Machine when she uses it to learn the unhealthy habits of her psychiatrist, Dr. Carmichael ( Bruce Altman ).

2. Nothing to Hide

Wayne Kruger ( David Alan Basche ) is the owner of a company known as Lifetrace, which specializes in revealing members' privacy on their profile pages and selling it to various organizations. Reese, Finch, and Shaw monitor Kruger's activities in the company, which is currently making a deal with another large retail company called Riverton. Though the site is deemed harmless by Kruger, Finch discovers that there is a class-action suit against Kruger involving various victims of the site whose privacy has been eliminated. Members of the suit receive anonymous packages containing information on how to humiliate and attack Kruger in revenge for their lives being destroyed thanks to Lifetrace.

One of these people is Stu Sommers, a man whose daughter was stalked and killed by her ex-boyfriend after he used Lifetrace to follow her. Reese convinces Sommers not to kill Kruger before being shot at by Collier, a man supposedly working for Riverton. Collier also kills Kruger before fleeing the scene. He was the one who sent the anonymous packages.

3. Lady Killer

When the Machine gives the number of Ian Murphy ( Warren Kole ), a man suspected of being a stalker, Reese along with Shaw recruits Carter, Fusco and Zoe to investigate further into his background. But when they discover that Murphy has a son from a former lover who is now dead, they work to reunite the boy with his father and right the wrong set in motion by the boy's grandfather, who wanted Murphy dead after he did not approve of him and saw him at his daughter's funeral. Meanwhile, Root sets her escape plan in motion with the help of the Machine when government operative Hersh tracks her down. Finch arrives at the hospital and finds to his horror the hospital staff incapacitated and Root gone.

4. Reasonable Doubt

Reese and Finch's next number is that of Vanessa Watkins ( Kathleen Rose Perkins ), a prominent New York prosecutor who is accused of killing her defense attorney husband, Jeremy. The police find a gun with her DNA on it and arrest her. Vanessa escapes police custody. Finch investigates Jeremy's murder and learns that he owed money to a gangster. Reese, Finch and Carter question Watkins to decide if she is guilty or innocent. Her testimony eventually convinces them that Vanessa is innocent, but they also discover that Jeremy, who turns out to be alive, has emptied his bank accounts.

They then conclude that Jeremy framed her and Reese drops Vanessa at a bus station to flee as Jeremy may try to kill her. But the team discovers that Vanessa lied in the testimony, had a fake passport for herself and did not leave town, intending to kill Jeremy. On his yacht, Jeremy is held at gunpoint by Vanessa. Reese arrives, leaves his gun next to Jeremy and leaves. Reese then has Finch call the authorities as gunshots are heard from the yacht, not revealing who survived or died.

5. Razgovor

In a series of flashbacks to Shaw's childhood it is revealed she was in a car with her father when he was killed in a wreck, but that she showed a lack of emotion over it. In the present, Shaw saves another number. The team's next number turns out to be a Russian immigrant girl named Genrika Zhirova (Danielle Kotch), who is deeply interested in espionage and is living with an older cousin in a run-down apartment. Shaw ends up watching Genrika when men come to attack her. Genrika had been bugging the phones in her apartment building and overheard information she should not have.

Meanwhile, Carter is continuing her investigation of HR. She is eventually asked to meet her partner Laskey at a bar, where he confronts her about her work with Reese. Knowing that Laskey is corrupt, she blackmails him into working for her. Root later arrives at Shaw's loft and abducts her.

6. Mors Praematura

While Shaw is abducted by Root, Finch and Reese get the number of Timothy Sloan ( Kirk Acevedo ), an estate investigator. Finch goes undercover as Sloan's assistant while Reese continues investigating Shaw's whereabouts. Sloan investigates the case of his foster brother, a man named Jason Greenfield ( Michael Esper ), who apparently died of a heroin overdose. Finch soon learns that Greenfield used to be a member of the organization Vigilance, which includes Peter Collier ( Leslie Odom, Jr. ) (from the episode "Nothing to Hide"). Meanwhile, Shaw reluctantly agrees to help Root get into a CIA black site.

Jason, who is alive, is one of the people held there, awaiting transfer. The transfer is intercepted by Vigilance, leading to a shootout. Root helps Jason escape and tells him to go to a location in South America. Reese and Shaw eventually save Sloan and recapture Root, but Collier gets away. Finch locks up Root in the Library.

7. The Perfect Mark

Reese and Finch get the number of Hayden Price ( Aaron Staton ), a hypnotherapist. Finch, who poses as Hayden's patient, learns that Hayden is a con man who hypnotizes his patients into giving him their security information, which allows him to enter their bank accounts and steal from them. One of his patients, Sven Vanger ( Carsten Norgaard ), is in fact a money launderer for HR who bids fake items at auctions. One of the items he purchased is a baseball signed by the 1922 New York Yankees team, which is worth $4,000,000. Sven sells it for $5, believing it to be a fake.

That night, Laskey shows Carter the pictures he has taken of Simmons' activities, when Terney comes in with his gun drawn. Terney shoots Laskey dead, and Carter responds by shooting Terney almost immediately after. She begs a dying Terney to tell her if the head of HR is in one of Laskey's pictures, and Terney places his bloodstained finger on the picture of Alonzo Quinn.

8. Endgame

Finch receives 38 numbers, all members of HR. Carter intercepts a drug delivery of the Russian mob, causing leader Peter Yogorov to suspect HR. Carter starts a war between HR and the Russians by firing sniper shots at HR leader Alonzo Quinn, who blames the Russians. Quinn orders his right-hand man, Simmons, to have his men round up the Russians. Reese learns about Carter's plan, and Finch deduces Quinn's identity as the head of HR. The Russians' numbers come up as they are now threatened by HR, but both groups are arrested by the FBI when Carter tips them off.

Carter takes Yogorov into protective custody and has him sign a statement that can earn an arrest warrant for Quinn, but the judge she approaches is member of HR. Quinn, Simmons, and two other HR cops wait for Carter at the judge's house, where Carter reveals that she called Reese and Finch, recording HR's incriminating conversation. Reese breaks in, a shootout ensues, and Carter apprehends Quinn. Simmons later accesses a dashcam that has a picture of Reese.

9. The Crossing

Reese and Carter are crossing town to deliver Alonzo Quinn to the FBI. Simmons alerts HR and several criminal groups of Reese's identity, limiting their means of movement. The two fight their way to, and break into, the city morgue. Simmons and Detective William Petersen ( Lee Tergesen ) capture and torture Fusco for the location of Carter's safe deposit box, which contains evidence against HR. To break Fusco, Simmons sends Lin ( Khalil Kain ) to kill his son Lee (Sean McCarthy); but Lin is killed by Shaw. Fusco breaks his own thumb to get free of the handcuffs, and kills Petersen.

Reese distracts the HR cops by killing or disabling all but one, leading him onto the street. Finch arranges for two honest policemen to arrest Reese to evade HR. Carter and Quinn reach FBI Headquarters. Quinn is charged with multiple offenses and HR gets disbanded, with the exception of a few rogue officers, including the now-fugitive Simmons. Carter, re-promoted to detective, releases Reese from police custody. Simmons fires on both Reese and Carter down the street. Carter shoots Simmons back, but he escapes, merely wounded. Severely injured, Reese holds a dying Carter in his arms as she loses consciousness.

10. The Devil's Share

Flashbacks illuminate Finch's dealing with survivor's guilt, Reese's time doing wetwork, Shaw's former life as a technically excellent surgeon but completely indifferent to the people she helped, and Fusco's recounting of exacting vigilante justice to a crook that slipped through the system (the devil's share). Reese starts sliding into his old, dark ways to get Simmons while also sliding towards death. Finch, Fusco, and Shaw go to an HR attorney to know Quinn's whereabouts to question him for Simmons' plan, but the Russians have killed him, shortly after Reese got the information.

The team turns to Root in desperation. Reese gets Simmons' location and is just about to kill Quinn when Finch reminds him that killing Quinn now would destroy Carter's legacy of bringing him down legally, and he collapses. Fusco finds the note that Reese dropped, and goes after Simmons. After a brutal fistfight, Fusco emotionally refuses to kill Simmons and takes him into custody, citing Carter's influence for turning his life around. Root, despite having opportunity to flee, returns to her cell, and Finch thanks her for helping him in saving Reese. Finally, Elias watches as Marconi murders Simmons in his hospital bed in retaliation for Carter.

11. Lethe

Reese leaves the team and heads for Colorado, where his father had lived. The Machine provides a new number to Harold, who at first is reluctant, but eventually accepts it on Root's insistence. The number belongs to Arthur Claypool ( Saul Rubinek ), Harold's close friend during his days at MIT. Claypool has been diagnosed with a brain tumor and is being monitored at the hospital, being kept under Secret Service guard. Arthur's wife, Diane ( Camryn Manheim ) tells the disguised Doctor Shaw that Arthur works for the NSA, and Collier's group Vigilance tries to abduct him.

They escape to a hotel, where Harold talks to Arthur to get more information about Samaritan: a project which sought to build an AI, like the later Machine, but was shut down just as it achieved consciousness. As Arthur talks with Finch, he remembers that his wife is dead, prompting the woman pretending to be Diane to reveal herself as Control. She threatens to kill either Arthur or Harold unless one of them gives up their respective AI. The Machine starts analyzing threats to its assets and itself, changing Samaritan's status from "Deactivated" to "Unknown".

12. Aletheia

Control holds Harold, Shaw and Arthur captive. She orders Shaw killed, but Root enters, guns blazing, and frees the trio. Root herself is shot and captured by Control, who tortures her, demanding access to the Machine. Control destroys the hearing in Root's right ear and threatens to make her completely deaf and blind. Meanwhile, Arthur reveals that he has a copy of the Samaritan AI in a safe-deposit box. They go to retrieve it, and Vigilance militants attack the bank. Harold locks himself, Arthur, and the bank manager in the vault.

While Shaw readies a bomb to break out of the vault, Harold tells Arthur about the Machine and convinces him to destroy Samaritan to keep it from falling into the wrong hands. Vigilance breaks into the vault and captures everyone, including Shaw, but Reese and Lionel save them. Meanwhile, the Machine helps Root to escape from Control. Root calls Harold to tell him that the Samaritan drives were not destroyed: The bank manager was an imposter who swapped the disks with replicas. The impostor is shown handing the drives to Decima Technologies head Greer, who shoots her to cover his tracks. He has great plans for Samaritan.

13. 4C

Reese boards an international flight to get away from his former life, but the Machine makes changes to his itinerary causing him to take another one. Initially Reese is angry at Harold thinking he has made the changes, but Harold convinces him otherwise. It turns out that Owen Matthews ( Samm Levine ), a passenger on the plane is a witness being escorted by U.S. Marshals, and he is the intended target of multiple assassins including the ISA. After Reese foils several assassination attempts, Finch learns that one of the assassins plans to crash the aircraft and kill everyone onboard just to ensure the witness is eliminated.

Reese and Harold safely land the plane and save everyone, and all ends well. Reese goes on a date with Holly ( Sally Pressman ), the flight attendant who helped him and later tells Harold he wants a new suit and to come back and work again.

14. Provenance

The team's next case is that of Kelli Lin ( Elaine Tan ), a former silver medal-winning Olympic gymnast who is later revealed to be an antiquities thief long pursued by Interpol. Shaw investigates Kelli's house, learning that her next operation is to steal a Gutenberg Bible that is being shipped out that night. Shaw foils the plan but is confronted by Kelli, whose boss Cyril ( Gene Farber ) is an extortionist revealed to be forcing Kelli to commit robberies while her daughter is held captive. Finch takes Interpol agent Alain Bouchard (Henri Lubatti), the man in charge of the investigation against Kelli, to listen in on Kelli's conversation with Cyril so Bouchard can learn the truth.

Cyril refuses to free Kelli's daughter, but sees Reese take down the thugs guarding her on the surveillance feed. Shaw stops Cyril from killing Kelli and both Kelli and Cyril are apprehended. In an interrogation room at the NYPD, Bouchard places a key on a desk, allowing her to leave. The next day, Kelli and her daughter happily reunite. That night, the team celebrates their victory and Reese honors Carter by pouring a glass for their "missing member".

15. Last Call

When the number of Sandra ( Melissa Sagemiller ), a 911 operator, comes up, Harold goes undercover at the 911 call-center. Later, a child is kidnapped and the call is routed specifically to Sandra. She is ordered to delete an earlier day's 911 call logs, in return for the child's life. Meanwhile, the case overlaps with one of the murder cases with which Fusco was helping a rookie detective. It turns out that a woman was killed by her married ex-boyfriend and boss, and the family hired a cleaner to erase the final 911 call she made.

When Fusco 'convinces' the family to terminate the contract, the cleaner decides to kill both the child and Sandra. Reese and Shaw save the child from kidnappers and a bomb, while Harold traps the assassin who comes after Sandra. The team is never able to find the real cleaner, who later calls Finch to threaten him. The criminal becomes known as "The Voice".

16. RAM

In 2010, Harold works with Dillinger ( Neil Jackson ), an ex- Blackwater mercenary who performs the same duties later performed by Reese. Their current number is Daniel Casey ( Joseph Mazzello ), a hacker who tests computer security systems. Multiple parties attempt to eliminate Casey, including Reese and Stanton (secretly arranged by Control) and agents of Decima Technologies. Dillinger saves Casey and brings him to Harold, who realizes Casey's last job was to find a way to access the Machine. Although Casey failed, he learned enough to warrant Control to want him dead and his laptop destroyed.

Dillinger turns on Finch and steals the laptop from him to sell on the black market, but not before Finch modifies the laptop's code. The sale is busted by a Special Counsel agent (Shaw) who kills Dillinger, but one of the buyers escapes with the laptop. Casey is captured by Reese, who decides to let him live against his orders, providing him with safe passage to Canada, an act of mercy that Harold observes unseen. Control traces the laptop to China, and orders that Reese and Stanton to be sent after the laptop and destroyed along with it. In the present day, Root finds Casey in Alaska and tells him to go to Cartagena, Colombia and seek out Jason Greenfield.

17. /

The Machine orders Root on several tasks such as helping a convict escape and using him to impersonate a Department of Defense employee in order to obtain a secret note. Afterward, she and Harold's team coincidentally reach the same person, a janitor. It later turns out that NSA has been testing an advanced supercomputing chip and the janitor was one of the 15 people who had access to the development lab. This makes both Decima and Vigilance come after him. While Harold and his team's assignment was to protect the janitor, Root had to stop the chip from falling into Decima's hands. They are able to save the janitor, but Decima gets the chip.

18. Allegiance

The team receives the number of Maria Martinez ( Nazneen Contractor ), an engineer working for the international energy company HydralCorp. Maria is working to clear the name of Omar Risha ( Haaz Sleiman ), a man from Iraq suspected of being a terrorist. Shaw, Fusco and Reese save Maria from an assassination attempt and learn that Omar was her translator in Iraq and saved her from a terrorist ambush during the shipment of six generators. The generators went missing and Omar learned about their disappearance, being targeted for it. Finch learns that the generators were shipped elsewhere and that HydralCorp's corrupt CEO Ken Davis ( Casey Biggs ) is responsible.

Maria and Shaw discover that Davis has created a false report of Omar's terrorist accusations, and that French United Nations diplomat Rene Lapointe ( Michel Gill ) has the papers approving Omar's asylum in the US in his office. Reese, Fusco and Omar break into the UN building and stop Greek diplomat Christos Sevon ( William Abadie ) from killing Maria. Root takes Bear to spy on Decima head Greer, where it is revealed that Davis had the generators shipped to the US so Greer can power Samaritan. Greer has Davis killed and leaves, and Root follows him.

19. Most Likely To...

The team witness Leona Wainwright being killed by a suicide bomber. She worked for the government, managing security clearances; Finch deduces from cell phone information that Vigilance killed her. Their next number, prosecutor Matthew Reed ( Nestor Carbonell ), sends Reese and Shaw to a high school reunion in Westchester. They manage to prevent a planned murder, while fending off an ambush by Vigilance. Meanwhile, Finch and Fusco go to Washington, D.C. to find out why Leona was targeted, but Vigilance beats them to it. Collier obtains classified documents about the Machine and disseminates them world wide. Senator Ross Garrison ( John Doman ) publicly denies the existence of the Machine and orders Control to shut it down. She gives the command, and shreds Collier's eyes-only file. With its Primary Operations compromised, the Machine restructures, transferring massive amounts of red-flagged data to Tertiary Operations: Root.

20. Death Benefit

The new number is Congressman Roger McCourt ( John Heard ), who serves on the powerful Rules Committee. The team is initially baffled: He has no obvious enemies. They eventually discover a connection to Decima: McCourt admits to agreeing to help Decima with favorable legislation (granting Decima access to government surveillance feeds), in exchange for insider stock-trading tips. Reese concludes that the team is the “danger”, because the Machine wants them to kill McCourt in order to prevent future killings by Decima. Harold is deeply disturbed at this idea, and he leaves the team, not wishing to participate in an assassination.

In the end, McCourt is left alive and proceeds with Decima's plan. Greer also approaches a skeptical Senator Garrison, offering him a 24-hour beta test of their machine. Garrison agrees, and Greer immediately deploys Samaritan to track down Finch. Meanwhile, Root is travelling across the country, dealing with various relevant threats.

21. Beta

With Finch having disappeared, Decima initiates their plan with Samaritan, and when unable to find Finch, they look for his closest connection and the number received is that of Finch's fiancee Grace. The Machine also provides Grace's number as a result, and Reese, Shaw and Root work to protect her while evading Decima, who use Samaritan to spy on them within the range of New York. Grace is eventually kidnapped and interviewed by Greer, who reveals his extensive knowledge of her and begins asking about her life with Finch. When he implies that Finch lied to her, Grace snaps and firmly tells Greer that Finch would never lie as Grace gave him her unbreakable trust.

When the team manages to locate Decima's current HQ, Greer takes Grace and tells Reese and Shaw that they can get Grace back in exchange for giving them Finch. Finch agrees to the deal, and at Jefferson Bridge, Grace is blindfolded and brought to Reese and crew while Finch is taken by Decima. Reese later gives Grace an envelope, saying that she has been accepted for a job in Italy. Greer, meanwhile, finally meets Finch in person and sits down with him to talk.

22. A House Divided

In a series of flashbacks to 2010, the narrative reveals the backstory on Collier, the face of Vigilance. His brother had been falsely accused of terrorist activities, held without trial, and had committed suicide as a result. The Machine's latest numbers include Control, Senator Garrison, a presidential assistant, and a seemingly unconcerned Greer. Vigilance kidnaps them, along with Finch, and the episode ends with Vigilance about to conduct a private trial of their detainees, while Reese and Shaw, along with Hersh (joining forces after a tense confrontation) watch from a closed-circuit TV screen set up for their benefit. Meanwhile, Root has discovered the location of the Samaritan system.

23. Deus Ex Machina

The trial continues. Reese, Hersh and Fusco search for the courtroom. Shaw helps Root smuggle seven servers into the Samaritan array. Hersh finds a bomb, wired to go off when the power comes on. Control is found guilty. To save her life, Finch confesses to building the Machine. When a command post is compromised, Collier moves the trial to the roof, where Decima attacks. Greer reveals that he himself created Vigilance. He wanted an atrocity—the bomb—to justify Samaritan. The bomb explodes, Greer's lieutenant kills Collier, and Reese rescues Harold. Because of Samaritan, Vigilance members are identified, targeted and eliminated, but Harold's team is identified as “irrelevant” by the program. Finch, Reese, Shaw, Root and the programmers have new identities. The seven servers hard-wire Samaritan to ignore them. Samaritan asks for instructions. Greer replies, “What, my dear Samaritan, are your commands for us?” The answer: “Calculating response... ".