The Machine monitors the series of events leading to Reese's arrest and imprisonment at Rikers Prison.
Carter interrogates Reese while Special Agent Donnelly monitors the exchange from the adjoining room. Reese remains silent despite Carter's warning that as long as he remains unidentified, they can hold him as an enemy combatant without access to legal counsel.
Back at headquarters, Finch calls Fusco and tells him that he will have to protect their newest Number because Carter is otherwise occupied. Fusco isn't particularly interested until Finch sends him photos of the Number: supermodel Karolina Kurkova.
Carter interrogates Reese and the three mercenaries. The mercenaries all have cover stories and Reese claims that he's an investment banker named John Warren. He professes his innocence and tells Carter that he hopes she believes him because she's his only chance of getting out.
The FBI sends a memo to the Special Counsel in Washington asking about his connection to the "man in the suit. He calls Hirsch, his operative in the field, and tells him that the rogue operative they're looking for is one of the four men imprisoned at Rikers. Hirsch decides to eliminate all four to be on the safe side and then fires his gun into the sky while standing at an outdoor cafe. Two policemen easily capture him, just as Hirsch planned.
Warden Hutchens complains to Donnelly that the special agent is violating the prisoners' rights, but Donnelly points out penal violations that he's seen and tells Hutchens to deal with those and leave him alone. Carter suggests that they uncuff the prisoners so that she can win their trust and Donnelly reluctantly agrees. They go over the cover stories of the four prisoners and confirm that three of them are from out of state. Reese's cover ID works on Wall Street and Donnelly decides to go there immediately to check it out. As they leave, Carter texts Finch, who assures her that she has nothing to worry about.
When they get to the office, Donnelly discovers that there is indeed a man named John Warren who works there. There are photos of Reese and his parents in a corner office and the secretary wonders where Reese has been for the last few days. Carter calls Finch privately and he assures her that that the Warren ID is the most secure cover they have for Reese. However, their entire operation will be jeopardized if Donnelly finds any flaw in it. Carter warns Finch that the three mercenaries are remaining silent because they figure they're being charged with murder. Once they realize Donnelly wants Reese, one of them will give him up. She suggests that they frame one of the mercenaries as Reese and Finch assures her that he's working on it. He's also working on an escape plan and checks in with Fusco. Karolina has spotted Fusco following her and has started macing him, and Finch leaves the detective to his own devices and tells Carter he'll handle the escape on his own.
Donnelly checks in with Carter and admits that "John Warren" appears real. However, he's still not convinced since he figures they're dealing with a powerful covert intelligence operation. The special agent gives Carter an earpiece so that he can secretly feed her questions when she goes back to interrogating the prisoners and tells her to increase the pressure.
Reese and Kara Stanton kill an American traitor selling drone blueprints to two Chinese nationals, and kill the nationals as well. When Kara cracks a joke, Reese ignores it and she tells him to lighten up. She warns him that he'll have to accept the fact that he's a killer and that he might as well learn to love his work.
In the interrogation room, Carter asks Reese if he's killed anyone. After questioning her on the same point, he talks about how he was in Bosnia and killed a Serb militant who was planting mines. When Reese claims he's reluctant to talk about it, Donnelly tells Carter to keep pushing. Carter asks Reese about his parents and he tosses out various details, all of which prove valid when Donnelly checks. Reese asks Carter where she served and they chat, and Donnelly calls Carter out to complain about her friendly approach. She insists that she's trying to build a rapport and Donnelly admits that Reese's story checks out.
While the guard brings Hirsch into Rikers, Carter continues interrogating the four prisoners. They finally manage to identify one prisoner, Brian Kelly, as ex-military. However, Donnelly has to release him to a cell since now that they identified him, they can't hold him incommunicado as an unlawful combatant. The special agent has confirmed that Kelly has an alibi during the New Rochelle murder and figures they can eliminate him as a suspect.
In the exercise yard, Reese is released and one of his former adversaries, Byron, comes over with his skinhead gang. Byron wants his dog back and prepares to attack Reese for sending him to prison, but another prisoner stops him. Byron and his men wander off and the prisoner takes Reese over to his boss: Carl Elias.
Reese and Kara go to a bar in Paris and target a couple. They have orders to kill the couple and Reese wonders why, but Kara isn't interested. As they watch the couple flirt, Kara suggests that Reese might play along with their own cover and kiss her occasionally. Once the bar clears out, Kara shoots out the camera and Reese goes over to kill their targets.
Elias takes Reese to a camera dead-zone, well aware that Donnelly is watching, and admits that he still appreciates Reese for coming out of nowhere and saving his life. Reese tells him not to protect him since Donnelly thinks that the man in the suit is still connected to Elias, and points out Hirsch. Elias is glad to have someone take Hirsch out but Reese warns the crime lord that Hirsch could be as dangerous as he is. He suggests that Elias get a photo of Hirsch to Finch and Elias agrees.
The Armenian mobsters on Karolina's trail try to intercept her as Fusco takes her to the police station. As they hide, Finch calls Fusco and sends him a photo of Hirsch to identify. Fusco recognizes the government operative from when he's been at the station looking into Corwin's death. As Fusco starts to ask for help, Finch hangs up.
At Rikers, Donnelly tells Carter to keep pushing Reese on his vulnerable spots. When she asks why he didn't reenlist after 9/11, he explains that he was afraid that if he went back into the Army then he'd never learn to do anything else. Donnelly continues to check all of the information that Reese is providing, including Reese's alleged superior "Howard French." The special agent is unaware that Finch has hacked Carter's earpiece and is hurriedly creating electronic records to match Reese's improvisations.
One of the remaining prisoners, Charles Macavoy, asks to talk to Carter. She goes in and he wants to rat his fellow prisoners out before they rat him out. Macavoy asks for immunity and Carter starts to haggle, but Donnelly storms in and tells Macavoy most of what they know about the man in the suit. Carter objects, warning Donnelly that he's giving too much away, but the agent figures that they can shock and awe Macavoy into giving himself away if he is there target. Macavoy doesn't know anything about Donnelly's accusations and the agent agrees to give him immunity in return for information on the man in the suit. Before Macavoy can agree, the fire alarms go off and the guards get the prisoners out into the exercise yard. Finch tells Carter over the earpiece that he set off the alarm and she should put her phone in Macavoy's pocket.
When Macavoy gets out in the yard, Finch calls him and relates all of the details of Macavoy's family as well as the $6.2 million he had hidden in an offshore bank account. Finch removes the money and tells Macavoy that he can either deal with him or Donnelly. Meanwhile, Hirsch goes to Kelly's cell and strangles him, then strings him up by the bed sheet.
When Macavoy is back in the interrogation room, Donnelly gives him his immunity deal and shows him photos of Reese and the other mercenary, Wayne Packer. Macavoy picks out Packer but Donnelly notices that he's now sweating and figures that someone got to him. Out in the hallway, Donnelly tells Carter that Kelly apparently killed himself. He figures that his target's organization set off the alarm, killed Kelly, and got to Macavoy. Since Macavoy fingered Packer, Donnelly figures that his real target is Reese.
After finishing their assignment, Reese and Kara go back to their safe house and clean out the place. Kara suggests that they take time off before their next assignment and he says he's fine. Upon hearing that, Kara slams him against the wall, shoves a gun in his face, and tells him to choose whether he is going to be a killer or not. She reminds Reese that he was the one who chose to become a killer. Smiling, Reese swings her against the wall, says he loves his work, and kisses her.
Donnelly sends Carter back in to break Reese, and she asks why he left the military. Finch tells her to slow down so that he can keep generating fake records to back up whatever Reese comes up with. Forced to stall, Carter agrees to trade information and answers Reese's earlier question about if she ever killed anyone. She describes how she shot a supposed insurgent in the Middle East during a raid but was never sure if he was innocent or not.
Once Finch is ready, Carter asks Reese if he's ever been in love. He gives a fake name but describes what really happened to him on 9/11 when he and Jessica were in a hotel room at Niagara Falls and found out about the 9/11 attacks. Reese wanted to re-up but realized that he'd never have a life with Jessica if he did. However, he tells Carter that he let her slip away anyway and wonders what his life would have been if he had gone back into the army.
Once she has everything she's going to get, Carter checks with Donnelly, who still isn't convinced of Reese's innocence despite the weight of evidence supporting his claims. He says that he has one last test and then has the guards take Reese back out to the exercise yard. As Donnelly and Carter watch on the cameras, Donnelly tells her that he plans to let Byron and his gang go at Reese again. The agent figures that Reese will crack and use his combat skills to defend himself. Hutchens objects but Donnelly overrides him and tells the warden to get all of the guards out of the yard.
Byron and his men come after Reese, who puts up a token fight and nods to Elias' man to stay out of it. The Aryans beat Reese to the ground, unaware that Hirsch is moving in with a hidden knife. Elias spots the killer and steps in, telling Byron and his people to back off. In the office, a disgusted Carter tells Donnelly that what he's doing isn't right. She storms out to interrogate Packer, claiming that Kelly and Macavoy made a deal. He finally gives up his real name and asks for a lawyer, but Carter continues to pressure him. When she finally convinces him that she's going to put him away, Packer tries to strangle her and the guards quickly come in and pull him away. Carter leaves the room and tells Donnelly that Packer is his man.
A little later, Finch is loading up on guns when Carter calls to tell him that they won't need an escape plan after all. She then meets with Reese near the river. When he asks where Fusco is, Carter tells him that Finch has her partner working on something else.
Fusco and Karolina are hiding behind a car as the Armenians fire at them. The detectives tells Karolina to run. She's reluctant to leave her savior behind but finally runs away while Fusco comes up, both guns blazing.
Reese thanks Carter and admits that he couldn't have made it through the interrogation if there wasn't a friend there to talk to. She asks if any of what he said was true. However, before Reese can answer, Donnelly shows up and captures them at gunpoint. He congratulates Carter on finding the real man in the suit and orders both of them to drop their guns. Once they're both handcuffed, a disgusted Donnelly tells Carter that she just threw away her career, and that she was the one who gave Reese away.
In Morocco, Reese and Kara meet with Corwin and Snow to get their next assignment. After being told that they're heading to China to recover a laptop with stolen Pentagon source codes, Snow talks to Reese privately and tells him that he's to kill Kara. As Reese leaves, Kara notices him smiling, says that it's been a while, and tells him that she needs him to be a killer.
In China, Reese prepares to shoot Kara as they wait for pickup. He finally chooses not to and Kara shoots him instead. Laughing weakly, he tells her that they both had the same orders and then runs as the U.S. bombs the town.
Once the Armenians are defeated, Karolina thanks Fusco for his help and gives him a kiss, and asks him to call her. Finch calls to tell Fusco that they have an emergency and sends him to Carter's last known coordinates. As Finch heads for the coordinates himself, a nearby payphone ring. Realizing that it's The Machine, he ignores it. However, all the other phones on the street start ringing. Finch picks up one phone and The Machine gives him a coded Number.
Donnelly loads Carter and Reese and drives them to a safe house. He informs them that he doesn't know who to trust and has no backup, but he knows someone in Justice that can deal with them. Donnelly explains that he suspected Carter after the DNA and fingerprint evidence disappeared, but he was sure when he saw the concern in her eyes when the Aryans beat Reese. Carter insists that she was just trying to help a friend and that Reese is a good guy, but Donnelly dismissively says that Reese is a killer and that he chose to become a killer.
Back at headquarters, Finch deciphers the code and discovers that the Social Security number belongs to... Donnelly. He calls the agent on his cell phone and tells him to stop the car. As Finch tries to explain to a confused Donnelly that he's in danger, a semi rams into Donnelly's car, running it off the road. All three people inside are injured and trapped in the wreckage. Kara gets out of the semi, comes over, and shoots Donnelly in the head. She then injects Reese with a sedative and asks if he missed her.