Carter is at work when Finch calls to tell her that Reese is downtown and needs her help. As she heads out, Special Agent Donnelly arrives and says that he needs her, and won't take any excuse from her. He takes her to the FBI command center and shows her that they've spotted Reese on a CCTV.
Three Days Earlier
Reese and Finch meet at their headquarters and Finch tells his partner that he'll have to hold off on helping Fusco with HR because they have a new Number. The Number is Caroline Turing, a psychologist who deals with high-end clients that demand discretion. Reese starts following Caroline, cloning her phone, and receives a call from Fusco. Fusco wants backup for his upcoming sitdown with the HR head men, and Reese tells him that he'll be there and that meanwhile Fusco should check on Caroline.
Caroline is meeting with a client, prosecutor Hans Friedrickson. Reese listens in from across the street as Hans complains that he's not sure if he should have told her some of the things that he has, and that he's worried it could put them both at risk.
Simmons and Fusco go to a restaurant to meet with the three HR superiors: Councilman Larsson, Captain Peter Lewis, and Detective Romano. After they joke with Fusco a bit, they invite the two men to sit down and explain that they've been paid to kill someone by a rich man. Simmons assures them that his people can handle it while Fusco runs interference in Homicide. Fusco fishes for the name of the client, but Simmons tells him that it's need-to-know. He does ask if they can trust their client and Larsson says that they already have the fee upfront. Larsson pays off Simmons and gives him a photo of the target: Caroline.
Caroline finishes her session with Hans by telling him that she's referring him to another psychiatrist since he doesn't trust her. Meanwhile, Fusco calls Reese and tells him about the contract on Caroline.
That night, Reese slips into Caroline's office and plants a camera to ID her clients. Meanwhile, Finch gets Reese in to see Caroline posing as a new client. He claims that he's a consultant and she promises that she'll keep his secrets. After Reese asks her to close the blinds, they begin.
Finch is watching Simmons approach his killers and calls Carter. She's run a trace on Larsson's account and confirmed that someone transferred $500,000 into it from another account in the bank.
Caroline comments on Reese's paranoia, but he points out that she has a panic button and a new security system. She starts to speculate on Reese's background and Finch warns Reese over the earbud not to give anything away.
That night, Finch returns to the library, unaware that former NSA operative Alicia Corwin is following him. He then calls Reese and confirms that there's $5 million in the account and he's asked "fixer" Zoe Morgan to investigate further. She meets with Reese and informs him that the man ordering the contract is one of three men: Hans, who is out of town possibly setting up an alibi; Terrence Baxter, a banker being investigated for financial malfeasance; and David Sarkesian, a city official who supposedly slept with his intern.
Simmons trails Caroline and directs the killers, led by Jablonski, to her with orders to make her murder look like a robbery. As Caroline heads home that night, walking past a construction site, John "accidentally" runs into her. She figures that he's following her and suggests that he's paranoid. As Caroline tells him that she comes that way every night and it's safe, the killers come in from in front and in back. Reese knocks out one and kneecaps the others, and then quickly gets Caroline away. When she spots a police car and suggests they ask for help, Reese warns her that some of the police are the ones trying to kill her.
Jablonski calls Simmons and tells him what happened, and Simmons recognizes the description as Reese. He warns Jablonski that if he doesn't clean up after himself then he'll dispose of him rather than risk him turning state's evidence.
Reese takes Caroline to a hotel for safekeeping and has to pay $3,000 for the honeymoon suite since all the others rooms are booked. While Reese has Finch try to find an escape route, Caroline wonders why he's talking to thin air.
Carter watches on the monitor as the FBI pick up Reese on the CCTV.
At the hotel, Reese tries to work out if Caroline knows who the man who wants her dead is, and she admits that it could be any of his patients. When she panics, Reese offers her some chocolate to calm her down and tells her that he'll let her know when it's a good time to panic.
Detective Sagan with the NYPD is working with the FBI task force and explains that he spotted Reese on the CCTVs. They're figuring that Caroline is a hostage and confirm that he hasn't moved out of the area. As Carter looks around, she notices that Fusco is there as part of the joint NYPD/FBI operation.
Reese looks out the window and spots HR's killers moving in. Reese checks the hotel records and confirms that the previous penthouse resident was sent to jail for tax evasion but his helicopter hasn't yet been seized.
Sagan spots Reese and Caroline on the hotel cameras as they head for the roof. Brennan orders the NYPD to stay clear while he has his men go in. Meanwhile, Jablonski's team enters the building and tries to intercept Reese and Caroline on their way to the work. Before they can get there, Reese hears helicopters landing and realizes that the FBI are coming in by air. Finch directs them to a freight elevator, explaining that they can take it to the parking sublevel and then use an abandoned service tunnel to get to the old water treatment plant, and he'll pick them up there. Once Finch leaves their headquarters, Alicia breaks in.
En route, Finch texts Carter saying Reese needs her help. She secretly brings Reese and Caroline up on the monitors and then texts him to where he can avoid the FBI team.
Jablonski warns Simmons that the FBI are in the hotel, but Simmons tells him that they're after Reese, not HR. He assures the killer that they have an inside man who is guiding them to avoid the cameras and the FBI team. Simmons then sends Jablonski to the 25th floor with orders to blow the floor with Reese and Caroline on it, and let Reese take the blame.
Finch checks in with Zoe, who has confirmed that Hans is out of town on business... and has been for several days. She then tracks down Jimmy White, the man who was posing as Hans with Caroline. She explains that he was hired to pose as Hans and threaten Caroline, but he was blackmailed into it and doesn't know the person responsible.
Alicia enters the library and examines Finch's notes on their Numbers.
Reese and Caroline get to the freight elevator and check with Finch, who says that he's heading for the water treatment plant. He then checks with Zoe, who tells him what she's learned. She figures that something is wrong and goes to Caroline's office to investigate further.
As Simmons directs Jablonski and his men to the 25th floor, Carter spots them on the monitors and warns Reese by text message. As she does, she sees Fusco texting someone. Reese jams the elevator on 26 and has Caroline work to short out the wires so they can bypass the next floor. As Caroline works, she apologizes for thinking that Reese was paranoid. Meanwhile, Jablonski and his men plant the explosives on 25.
Brennan spots Reese on the cameras and has his men move in, and Carter warns Reese. The killers finish planting the explosives and wait for Simmons to give them the signal by cell phone. Realizing that the FBI have them cornered, Reese prepares to open fire... and Finch knocks out the nearby cell tower. Every cell phone in the area goes dead, keeping Simmons from signaling Jablonski and Brennan from reaching his assault team. Caroline bypasses the elevator controls and they head down. At the FBI command center, Carter sees Fusco get up and leave the room.
The FBI techs confirms that the cell tower has been sabotaged to white list every phone number except one. They spot Simmons on the monitors but he has his back to the cameras and shuts them off before they can identify him. Brennan decides to take his own squad in.
Carter warns Reese that she knows who is leaking his location to HR and then goes after Fusco. She finds him in the restroom, talking to someone on his cell phone. Carter draws her gun and orders him out, and he explains that he's working undercover against HR and that he's trying to turn his past around. Carter doesn't believe him until Fusco describes the two men that he's working for. She recognizes their descriptions and realizes that he's telling the truth, and Fusco explains that he was talking to Finch when she came in. Finch, who has been listening in, calls both of them to say that he'll explain later, but right now Reese needs their help. When Carter wonders who the real mole is, Fusco assures her that now that he's inside HR, he'll take them all down once Reese has escaped.
Reese and Caroline head for the service tunnel, and Reese spots the killers' car. He opens the trunk and grabs some extra weapons.
Come dawn, Finch gets to the water plant and tells Reese that he's there. Reese tells Caroline to head down the service tunnel to where Finch is waiting while he holds off Simmons and the others.
Alicia gets in the car with Finch and holds a gun on him. She tells him that they met years ago in Nathan's office when she thought he was an IT guy, and tells Finch that she wants him to shut down the Machine.
When the killers enter the sublevel, they exchange shots with Reese, who soon runs out of ammo. However, Carter and Fusco arrive in their car and open fire. The killers retreat and Reese gets in the car with the detectives as they drive off after Jablonski and the others.
Alicia tells Finch that Nathan was troubled about the Machine's power and it killed him as a result. She's spent years running from it and is tired. Finch admits that he's made some mistakes, but the Machine isn't one of them and it didn't kill Nathan. He warns her that the people that have been chasing her are the ones who now have the Machine, people they both trusted. Alicia admits that he's right and says she's lucky that she found Finch first.
As they pursue the killers, Carter and Fusco both demand to know why Reese didn't tell them about the other. He points out that they were both trying to capture or kill him at one point, and then tells Carter to hang back. Once she does, Reese triggers the explosive that he planted in the trunk earlier and they watch it blow up. Reese then tells the detectives they should get a drink sometime, gets out, and walks away.
Zoe breaks into Caroline's office. She spots a photo of a man on the desk, but discovers that it's been cut out from a magazine.
Alicia warns Finch that if the wrong person learned that Finch still has access to the Machine then he and it would both be vulnerable. Finch figures that she hired Simmons to kill Caroline to get to him because she knows about the irrelevant list, but Alicia has no idea what he's talking about. Before he can explain, Caroline arrives, shoots Alicia in the head, and gets into the car. She tells Finch that she's the hacker he went up against months ago, Root, and now they have a lot to talk about.
After checking Caroline's computer, Zoe calls Reese and tells him that the psychiatrist is a fake, and she's the one who paid HR to target her. Reese goes to the water plant and finds Alicia's corpse on the ground. There's no sign of Caroline and Finch.
As Brennan and his men go over the parking garage, the FBI agent receives an anonymous email with all of the evidence against HR.
At the police station, Fusco finishes sending the email and smiles in satisfaction at Carter.
Based on the evidence, Brennan arrests Sagan as the mole.
Simmons quickly walks out of the police station and goes to his car.
Reese checks in at headquarters but finds no sign of Finch. He then walks out onto the street and addresses a CCTV. He tells the Machine that Finch is in danger because he was doing its work, and it's going to help him back. After a few seconds, a nearby pay phone rings and Reese goes over to answer it.