Season 2

1. The Contingency

The Machine provides Reese a code that translates to the SSN of accountant Leon Tao, who is being targeted for stealing money from the Aryan Brotherhood. Reese saves Tao from the gang and adopts their dog, which he names Bear. The government sabotages Carter's investigation into Corwin's death to prevent her from learning about the Machine. Root takes Finch to a cabin in Maryland and kidnaps NSA operative Denton Weeks. She explains that she sees the Machine as a "perfect intelligence" and wants to "set it free." Reese threatens to quit his operations unless the Machine helps him find Finch, and receives the SSN of a girl in Texas who has been missing since 1991 when she was 14.

Flashbacks to the early days of the Machine's development depict it saving Finch from a distracted driver who dies in a crash. Finch rebukes the Machine and states that it should be protecting everyone, not only him.

2. Bad Code

Root interrogates Denton Weeks for the Machine's location and kills him after he discloses it. Reese identifies the missing girl provided to him by the Machine as Hanna Frey, who was abducted and never found twenty years prior. Reese suspects the missing Hanna to be Root, especially as her abductor was set up to be murdered in a manner matching Root's MO. Reese and Carter's investigation leads them to Hanna's friend Samantha Groves, the sole witness to the abduction. Sam informed the local librarian of what she saw, only for the librarian -- the perpetrator's wife -- to accuse Sam of lying and intimidate her into silence about the abductor's identity.

Sam later adopted the alias "Root" and left home after the death of her mother. With the help of the remorseful librarian, Carter finds Hanna's body and ensures that she gets a proper burial. While investigating Corwin's murder, Fusco finds a taped conversation regarding the government's search for Weeks, which, combined with a clue found in Hanna's killer's house, allows Reese to locate the cabin and retrieve Finch. Root escapes but calls Reese to thank him for finding her friend, but warns that she will come back for Finch.

3. Masquerade

As Finch tries to readjust to life after his kidnapping, establishing a bond with Reese's attack dog Bear, Reese poses as a bodyguard to get close to Sophia Campos, the spoiled daughter of the Brazilian consul in New York. Sophia has become the target of the leader of a drug smuggling operation, who believes that she and a friend witnessed their operations. Reese saves her from the gang. Meanwhile, Fusco hands the Alicia Corwin case on to Carter. While at the morgue, Carter encounters Mark Snow, who claims that he has been reassigned, but is in fact being held hostage by Kara Stanton.

4. Triggerman

Riley Cavanaugh, an enforcer for an Irish mobster, becomes the next number when he betrays his boss and goes on the run with his lover, Annie, whom he was ordered to kill. Reese and Finch debate the morality of trying to save a ruthless killer, but they soon need Riley's help when Annie is captured by bounty hunters hired by the mob. To keep Annie safe, Finch is forced to make a deal with Elias, who continues to run his criminal organization from behind bars, in exchange for a game of chess.

Elias uses his influence to order the hit called off, but the mobster continues to personally pursue the couple. Riley sacrifices his life in order to save Annie, an act Reese encourages her to interpret as proof of his love and a sign of his redemption. Reese later tracks down the hitman who killed Riley and presumably kills him in retaliation.

5. Bury the Lede

In the midst of New York's mayoral elections, the FBI are closing the net around the HR; 75 dirty cops are arrested, but their elusive leader remains unknown. Investigative reporter Maxine Angelis is trying to beat them to the story and becomes the next number, but Reese finds it difficult to openly protect Maxine when Finch discovers she is also researching an exposé on the mysterious "man in the suit". HR runs a gambit to trick Maxine into imprudently naming an FBI informant as HR's leader, causing HR's criminal enemies to murder the innocent man and discrediting all her work, including an exposé of a mayoral candidate.

Finch uses an online dating website to get Reese close to Maxine without exposing his true identity. While Reese helps Maxine hunt for the dead informant's ledger containing the names of everyone in HR, he must also protect her from repeated HR kill teams. Reese, Carter and Fusco track down the ledger, and Fusco secretly removes the pages that would incriminate himself and Simmons. The ledger names one of the mayoral candidates as the big boss, causing his opponent to win the race, but in reality, both candidates are on the payroll of Alonzo Quinn, HR's true leader.

6. The High Road

Reese ventures into suburbia to locate the next person of interest, Graham Wyler, whose past returns to haunt him. Reese "proposes" to Zoe Morgan for the mission to help blend into suburban life. They move to the suburbs to investigate Wyler. Wyler is forced to help with a robbery led by his former partners, as he is a master safecracker. He cracks the safe as Reese and the NYPD show up. Carter buys some extra time with the police by leading them up the wrong staircase to give Reese and Wyler time to escape down the other, but Wyler decides he does not want to continue running from his past and turns himself in.

He turns state's evidence against the gang and is then placed on house arrest, as the court deems him no threat to society due to his help in getting convictions on his crew. Flashbacks show Finch greeting Grace (his future fiancé) for the first time.

7. Critical

Reese and Finch work to save both the life of a CEO undergoing secret surgery and the wife of the surgeon from a former MI6 agent and a team of ex-SAS operatives. Leon Tao, once again in danger, assists while under protective detention. Carter handles the case of a murdered man with her business card in his pocket, discovering that Agent Snow is the murderer. Snow reveals to her that he has been strapped to a bomb suit and says that 'she', referring to Stanton, is planning something big. Detective Carter informs Reese of her meeting with Agent Snow, and he warns her to stay out of the case.

8. 'Til Death

The Machine produces two numbers belonging to a married couple who own a publishing house. Reese and Finch work together and soon discover that each has ordered a hit on the other to settle a proposed sellout deal for their company. Reese kidnaps the couple with Carter's reluctant help, and defends them from a group of armed thugs while Finch plays marriage counselor. Eventually the hitmen are taken down while the couple are arrested but work out their marital problems. Finch suggests that the two will not spend much time in jail due to skilled lawyers, as well as their refusal to testify against each other. Meanwhile, Carter begins a relationship with narcotics detective Cal Beecher.

9. C.O.D.

Reese works to save the life of a local taxi driver who is put in danger when a passenger leaves behind a laptop that is wanted by the Estonian mafia. Reese and Finch eventually realize the laptop contains valuable information that could enable terrorists to enter the country undetected. As a result, the Estonian mafia is killing anyone who has even seen the laptop. Finch is able to locate the laptop and the Estonians are defeated by Reese. Finch and Reese then have the cab driver use the laptop to negotiate a deal with the Secret Service to bring his family over from Cuba in exchange for the laptop.

At the same time, HR decides to reestablish ties with Elias and blackmail Fusco into helping. After walking into an ambush, Fusco tells HR member Simmons that Elias has cut all ties, and Fusco does the same. Unwilling to accept Fusco bowing out, Simmons leaves Carter with an anonymous tip that a cop murdered Detective Ian Davidson (" Blue Code ").

10. Shadow Box

Reese must protect the sister of a soldier who died in Afghanistan and her boyfriend, an ex-Marine who lost his right arm. The two are trying to expose an executive stealing from a charity for wounded veterans. Carter is offered a temporary assignment to the FBI when Special Agent Donnelly returns with new clues he believes will lead to Reese. The situation gets complicated when Reese, for whom the wounded veterans charity case has become personal, puts himself at risk as the FBI closes in on him while Finch is unable to stop him.

The FBI ultimately arrests Reese and three mercenaries under suspicion of being "the Man in the Suit," but the financial information recovered from a safe deposit box will allow Finch to redistribute the stolen money to reputable military charities; Finch promises to help the couple to escape to safety. Fusco, meanwhile, grows increasingly suspicious of Carter's boyfriend Cal Beecher, who is revealed to be the godson of HR leader Alonzo Quinn.

11. 2πR

With Reese in FBI custody, Finch poses as a high school teacher to protect the next number, a teenager named Caleb Phipps who is deliberately underperforming at school to hide his intelligence. Finch discovers that Caleb is a master coder and, with Fusco's help, learns the boy is also a drug lord. Finch accuses Caleb's tech teacher of stealing Caleb's code, but the truth is that the teacher is trying to promote Caleb's work so investors can help Caleb profit from it. Finch learns Caleb plans to give his valuable code and drug money to his drunk mother and commit suicide at the train station where his brother was killed in a train accident.

Finch is able to talk Caleb out of it. The next day, Caleb thanks Finch as he prepares for school, as Finch hints about his own past as a legendary hacker. Meanwhile, Reese and three other men are held captive by the FBI, who prepare to interrogate each one until they reveal the identity of the "Man in the Suit". In order to help prevent this, Carter removes Reese's fingerprints from the system and tampers with the DNA evidence.

12. Prisoner's Dilemma

Fusco is assigned to the new number, supermodel Karolina Kurkova. Meanwhile, Carter is asked to interrogate the four suspects in jail. Elias offers to help Reese, but Reese refuses, to avoid the attention of the FBI. Finch bribes a suspect to blame one of the other men, but after another suspect is killed by a government assassin named Hersh, Agent Donnelly suspects the real man is Reese. Donnelly incites a brawl involving Reese to get him to reveal himself, but Elias breaks it up, saving Reese and preserving his identity.

Carter questions the last suspect to provoke him, falsely identifying him as the man in the suit and securing Reese's release. Later, Reese visits Carter and thanks her, but Donnelly arrests Carter for conspiracy and Reese for murder, having deduced the truth from Carter's defense of Reese. The Machine informs Finch the next number is Donnelly and he tries to warn him as a truck hits Donnelly's car. Kara Stanton walks out, killing Donnelly and sedating Reese.

13. Dead Reckoning

Carter survives the crash while Reese is taken by Kara Stanton. Reese, with a bomb strapped to his vest like Mark Snow, is forced into doing fieldwork alongside him. The two steal a hard drive and are assigned to install it. A flashback shows Stanton was visited in the hospital by a man named Greer after surviving the Ordos airstrike. Stanton agrees to help Greer if he reveals who tried to kill her in China. Back in the present, Stanton activates the bomb vests and activates the cyberweapon stored on the hard drive; Reese and Snow escape, but Snow attacks Reese and runs off to get Stanton.

Carter and Fusco try to help Reese, but he refuses. Finch meets Reese and deactivates the bomb vest. Having completed her mission, Stanton is met by Greer, who gives her the name of the person who sold the laptop. Snow shows up in her car and his vest explodes, killing Snow and seemingly Stanton as well. The FBI later names Snow "The Man in the Suit" and closes the case. A flashback before the car explosion shows the name Stanton received: Harold Finch.

14. One Percent

Reese protects eccentric Internet billionaire Logan Pierce ( Jimmi Simpson ), who is dragging the reputation of his company FriendCzar through the mud with his bad behavior. After several attempts on Pierce's life, it is revealed that his partner, Justin Ogilvay, has been trying to kill him. Pierce flies himself and Reese to St. Petersburg, Russia, to escape the killer, but he invites several friends to join him and party, causing Reese to walk away. Pierce runs into Justin and his goons outside who are just about to throw him off a bridge when Reese appears and saves him.

Justin is arrested, and it is revealed that Pierce was in cahoots with Emily Morton, who has developed a superior technology. By being removed from FriendCzar, Pierce's non-compete agreement is void, allowing him to assist Emily in a new venture which will crush FriendCzar. When Reese shows Finch the $2 million watch that Pierce gave him, Finch stomps on it, revealing a tiny GPS tracker inside. Pierce was trying to track them and learn who they are. In a flashback to 2009, Finch's old partner Ingram is shown about to try to save one of the "irrelevant" numbers identified by the Machine.

15. Booked Solid

Reese and Finch work undercover in a hotel to protect a maid named Mira ( Mia Maestro ) who escaped the war in Kosovo. Mira, who is hiding her true identity, is being followed by a hit squad. She refuses to cooperate with a reporter investigating a Serbian general's war crimes. When the reporter is murdered, she decides to give a DVD with evidence to the authorities. Fusco escorts Mira to the station, where one final hit man attempts to kill her; he is shot by Carter. Meanwhile, Carter is invited to join the FBI.

She passes the polygraph but is rejected because Cal Beecher, her friend and love interest, has a record of Internal Affairs investigations. Acting on orders from the Special Counsel, Hersh follows Reese to the hotel, intending to interrogate and kill him. Reese stabs Hersh, and gives him a choice: Seek medical attention or attack Reese. Hersh chooses the hospital. While in recovery, he is ordered back to D.C. Finch purchases the hotel and promotes Mira to manager. Meanwhile, the Special Counsel's assistant, Miss May, is shown to be Root.

16. Relevance

The Machine gives the numbers of Sameen Shaw ( Sarah Shahi ), a government assassin, and Michael Cole ( Ebon Moss-Bachrach ), a computer specialist working for Special Counsel ( Jay O. Sanders ). Special Counsel has sent a hit team to eliminate Shaw and Cole because Cole may have obtained information on the Machine. They kill Cole but Shaw escapes, shooting Reese, who she believes is another assassin. Root captures and interrogates Shaw but leaves abruptly to avoid another hit team from Special Counsel. Reese saves her and Finch explains her "Research" does not actually exist, implying it is the Machine, and offers his aid to her, which she refuses.

She confronts Special Counsel, and returns the flash drive with the information Cole had recovered, then kills the subordinate who had ordered her and Cole's death. Special Counsel allows her to leave, but Hersh finds her and injects her with poison. Leon Tao (disguised as a paramedic), Carter, and Fusco take charge of the apparently dead body and drive away. Tao, as directed by Reese, injects her with an antidote. Shaw, fully recovered, meets with Reese and Finch in a graveyard and accepts Finch's card.

17. Proteus

After being silent for three days, when the Machine generates numbers of six missing people, Reese, Finch, and Detective Carter realize that they are hunting a serial killer who assumes the identity of his victims. Reese encounters FBI agent Alan Fahey ( Luke Macfarlane ) at Owen Island during his search for the same killer. Due to a severe storm, residents of the island take shelter in the police station. Finch arrives at the island and assists Fahey interrogate the people in the station. Carter, having researched the six victims, goes to help Finch and Reese.

Meanwhile, Finch and Reese discover that the killer is actually masquerading as Agent Fahey, whom he had killed before Reese arrived on the island. The killer captures Finch before Carter arrives and saves him before Beecher shoots the killer dead. Finch and Reese later ponder why the Machine was silent for three days, with Finch suspecting that the virus Kara Stanton uploaded to the Department of Defense has infected the Machine and slowed its abilities. He tells Reese that he believes this is the beginning of a coming storm.

18. All In

The Machine generates the number of watch repairman Lou Mitchell ( Ron McLarty ), who is consistently losing large sums of money at a casino. He and many other elderly gamblers are actually victims of a drug-money laundering operation headed by the casino's owner Dario Makris ( Michael Rispoli ). Finch breaks into the casino server room and gathers the needed evidence, but is caught and taken hostage along with Reese, Leon, and Lou. They are forced to play a game of Russian roulette, but Reese gets them out alive after Lou sneaks the bullet out before it enters the gun.

Meanwhile, HR incriminates Detective Szymanski ( Michael McGlone ) so the head of the Russian mob can be exonerated and give financial support to HR. Cal Beecher was the one who told IAB that Szymanski was corrupt, acting on information from one of Beecher's CIs. Carter succeeds in clearing Szymanski, but he is later killed along with the ADA by HR boss Alonzo Quinn, who makes it look like an assassination by an outside figure. Detective Terney ( Al Sapienza ) of the homicide task force is revealed to be an HR operative, potentially watching Fusco and Carter.

19. Trojan Horse

Reese monitors Michael Cole's family where Shaw finds him. Finch calls with a new number, that of Monica Jacobs ( Tracie Thoms ), a high-ranking employee of a technology company called Rylatech. Jacobs is being hunted and framed for industrial espionage by other employees who are secretly working as spies for China and Greer's shadowy company Decima Technologies. Meanwhile, Shaw tracks Finch to the library, where she grabs a list of Root's aliases from the wall, telling Finch she has a new project. While monitoring Beecher, Fusco discovers that he's innocent of any wrongdoing.

Meanwhile, Quinn realizes that Beecher knows too much about his role in HR, and arranges to have him killed. The Machine gives Finch his number, but too late for Carter and Fusco to save him. The next morning, Finch is taking a walk around town with Reese, telling him that he has identified Decima Technologies, the company which employed Kara Stanton to upload a virus onto the Machine. Unknowingly behind them, Greer is on the phone, and when he hangs up, he looks at his phone, which has a countdown ticking on it, and smiles.

20. In Extremis

When a highly decorated doctor named Richard Nelson ( Dennis Boutsikaris ) is poisoned with a fatal dose of radiation, Reese is forced to partner with Nelson to track down the killer after they both realize that the radiation has no antidote. Unable to save Nelson, the two poison the killer with the same toxin. Flashbacks explore how Detective Fusco became involved with HR and the development of his friendship with Detective Stills. Meanwhile, HR has an informant give the Internal Affairs Bureau the location of Stills' body so that they can send Fusco to prison in retaliation for him quitting.

Fusco confesses his past to Carter who is forced to evaluate her partnership with Fusco and how she might help him with the problems he is facing. With the help of Bear, Carter finds and moves Stills' body while Finch has Elias get the informant to recant. The Machine displays the coded blue screens with increasing frequency as it becomes apparent to Finch and Reese that the numbers are coming too late, leading to Dr. Nelson's death. As the episode ends, the Machine sends a series of alerts before beginning the process of shutting down its primary functions.

21. Zero Day

Special Counsel discovers that there is a threat to the Machine, which Finch and Reese are attempting to stop. The Machine gives a number belonging to Ernest Thornhill, a CEO who is buying several payphone companies in New York. Decima Technologies, Finch, Root, Shaw and Reese all attempt to reach Thornhill, but Finch discovers that Thornhill is an alias created by the Machine. Root and Finch enter Thornhill Enterprises and discover that the Machine will reboot to defend against the virus, once complete giving Admin access to who ever receives a call.

Reese and Shaw follow and encounter Greer and his men. Greer tells Reese that the laptop Reese had to recover with Kara Stanton from China was sent there by Finch. Finch knows which payphone the Machine is going to call and goes with Root to answer, followed by Shaw and Reese, where they encounter Greer's men. When the call comes, Root answers the phone, but Finch splices the call to a payphone near Reese so he too can answer the phone.

22. God Mode

The Machine grants both Reese and Root full administrative access and saves Reese (with Shaw) and Root (with Finch) from several potential threats. Root and Finch arrive at the Hanford nuclear facility where the Machine is kept, followed shortly by Reese and Shaw, the latter being slowed as the Machine directs them to rescue people from the irrelevant list. They find that the Machine has moved. Finch explains that he planted hidden code inside the Machine that would grant it the freedom to protect itself if it was at risk, code triggered by the virus from the Ordos laptop.

For failing to protect the machine, an unknown woman orders Hersh to kill Special Counsel. Meanwhile, Raymond Terney (HR) and Peter Yogorov attempt to kill Carl Elias. They are stopped by a masked Detective Carter, who wounds Terney and Yogorov and frees Elias. A payphone later calls Reese and Finch. Hersh talks with the unknown woman confirming that they received a relevant number. The Machine then calls Root. In flashbacks, Ingram plans to tell the press about the Machine, but Hersh manipulates a suicide bomber into detonating a bomb on a ferry where Ingram and Finch are meeting. Ingram is killed while Finch is injured. Grace believes Harold to have died in the explosion.