At the station, Carter receives a call from Finch telling her that Reese is downtown and needs help. He tells her that it’s an emergency and hangs up, and Carter heads out. However, Special Agent Donnelly catches her at the door and says he needs her, and won’t take no for an answer. He takes her to the FBI command center and tells Carter that they’ve spotted Reese.
Three Days Earlier
Reese meets Finch at the library and tells him that he’s been busy helping Fusco ascend the HR ladder. However, Finch tells him it will have to wait because they have a new Number, a psychologist named Caroline Turing. Finch has determined that she deals in high-end clients that want discretion. Reese follows Caroline and clones her phone as she orders coffee. Meanwhile, Fusco calls Reese and tells him that he’s meeting with the HR big shots, and wants backup. Reese tells him that he’ll get to it and wants Fusco to look into Caroline Turing.
Caroline is meeting with a client, prosecutor Hans Friedrickson, and Reese listens in as he complains that she doesn’t understand him. He’s worried that the things he’s told her could put them both at risk.
Simmons takes Fusco to meet with three of the heads of HR: Councilman Larsson, Detective Romano, and Captain Lewis. They warn him that they don’t tolerate malfeasance in cops and then break into laughter, and invite Fusco to sit down. They then say that they have a contract from a rich guy who wants a problem to go away and soon. Simmons assures them that all of his people are solid and Fusco will run interference from Homicide. Fusco warns that he needs names but Simmons tells him that he doesn’t and asks if they can trust their client. Larsson assures him that they already have the money and gives Simmons his payment. Fusco gets a look at the photo of the target and realizes that it’s Caroline.
Caroline tells Hans that she’s admitting failure and referring him to another psychiatrist, one who he can speak freely with. Fusco calls to tell Reese that HR has been paid to dispose of Caroline in the next 48 hours.
That night, Reese plants a camera in Caroline’s office, figuring that one of her clients hired HR to keep her quiet. Finch tells Reese that he’ll have to work through his issues, and Reese ends up making an appointment with Caroline. He claims that he’s a consultant and she assures him that she’ll protect his confidentiality at all costs. Reese asks her to close the blinds and they begin.
Down in the car, Finch calls Carter, who has traced a $500,000 deposit into Larsson’s account from an escrow account in the same bank. Finch takes the information while watching Simmons meet with some men. Meanwhile, Caroline points out that Reese is agitated and he responds by pointing out that she has a security system installed. She deduces that he’s former military and Finch, listening in, warns him to be careful. Caroline asks if he feels the need to protect people.
Later, Finch goes down the street and enters the library through a back entrance... unaware that Alicia Corwin is watching him. Inside, Finch tells Reese that he’s checked the escrow account. The transferee is untraceable but there is currently $5 million in the account. Finch tells Reese that he’s asked an old friend: Zoe Morgan. She meets up with Reese and explains that Caroline has kept a low profile. She’s narrowed the killer down to three possibilities. The first is Hans, who is out of town possibly to have an alibi. The second is Banker Terrance Baxter, who is being investigated for a possible Ponzi scheme. The third is David Sarkesian, a prominent city official supposedly sleeping with his intern.
Simmons starts following Caroline, reporting her route to the five killers that he’s hired. The killers are supposed to make the murder look like a robbery. As Caroline heads home that night, John intercepts her and she wonders if he’s following her. She suggests that he’s paranoid and assures him that there’s no one there and she’s safe. The psychiatrist tells him to go home and get some sleep, and the killers move in on her from both sides. Reese knocks out the one behind her and shoots the leg of the one in front of her, and then escorts Caroline away. He avoids the police and warns Caroline that the men after her are cops.
The head killer, Jablonski, call Simmons to tell them about the man in the suit who stopped them, and Simmons realizes that it’s Reese. When Simmons learns that Caroline got a look at Jablonski, he warns the hired gun that if he doesn’t clean up after himself then Simmons won’t risk him turning state’s evidence.
Reese takes Caroline to a hotel for safekeeping and pays $3,000 for the honeymoon suite. Simmons walks by outside as Finch works out an escape route. Caroline assumes that Reese is talking to himself and he doesn’t bother to explain about the earbud.
Finch calls Carter for help but Brennan takes her up and takes her to the FBI command center.
At the hotel, Reese asks who could afford to hire a team to take care of her, and she admits that it could be any of her patients. She panics and Reese offers her some chocolate and tells her he’ll promise to tell her when it’s time to panic.
Lt. Sagan with the NYPD explains that he picked up Reese and a young woman who appears to be a hostage, and they have him pinned down to a six-block area. Fusco is there, much to Carter’s surprise.
As they wait, Reese sees a HR police car pull up outside and Finch tries to work out a plan. He determines that the previous occupant went to jail for tax evasion but the IRS hasn’t seized his helicopter.
Sagan spots Reese and Caroline on the hotel cameras and Brennan tells the NYPD to hold off while he sends a FBI team in. Meanwhile, Jablonski’s team chases Reese and Caroline as they head for the rooftop helipad. They hear the helicopter outside and Reese realizes that someone else is coming in. He heads back down the stairs just ahead of a FBI assault team and calls Finch. Finch sends him to a freight elevator and tells him that he take it to the parking sublevel and use an old service tunnel to get to the old water treatment plant. As Reese heads for the elevator, Finch leaves the library and drives to pick him up. Once he’s gone, Alicia moves in.
Finch sends a text message to Carter saying that Reese needs their help. She brings Reese and Caroline up on the monitor and sends him a message to help him avoid the FBI team. Once they move on, she tells Reese to move.
Jablonski informs Simmons that the FBI is there, but Simmons says that they’re looking for Reese. He assures Jablonski that their man on the inside will give them Reese’s location and avoid the cameras. They have enough explosives to blow the floor, and figure they’ll take out Reese and Caroline and let Reese take the blame.
Finch checks with Zoe, who tells him that Hans actually is out of town on business. Hans comes out of a bar and Zoe approaches him, saying that his cell phone is registered to a short-con operator named Jimmy White. She figures he’s impersonating a prosecutor, and Jimmy admits that he was hired to threaten Caroline. He doesn’t know who hired him and they blackmailed him into it.
Alicia breaks into the library, shutting down Finch’s security systems. She then examines the board with all of the Numbers.
Reese gets Caroline to the freight elevator and contacts Finch, who says he’s moving into position. Finch then calls Zoe, who tells him that something is off. She heads back to Caroline’s office to see what she can find.
Simmons tells Jablonski and his men where Reese is, and Carter spots them on the monitors as they wait on the 25th floor. Carter sees them, and notices Fusco sending a text message. She signals Reese to get out of the elevator, and he hits the emergency stop on 26. Simmons warns Jablonski’s men and tells them to plant the explosives. Meanwhile, Reese has Caroline short out the wires and activate the bypass light. She apologizes for thinking he was paranoid while she works.
Brennan spots Reese on 26 and tells his men to move in. Carter warns Reese, while the killers plant the explosives and wait for Simmons’ signal. Reese tells Caroline to stay back while he holds them off... just as Finch takes out every cell tower in the area. Brennan and Simmons lose contact with their men, giving Caroline enough time to activate the bypass. Meanwhile, Fusco leaves the command center and Carter notices.
Finch has white-listed every number except his own and calls Reese. Meanwhile, the FBI surveillance techs pick up Simmons on the camera just as he cuts them off, and Brennan takes a squad of his men in.
Carter calls Reese and tells him that she has an idea who is feeding HR their information. She follows Fusco into the restroom and overhears him talking to someone, and orders him out at gunpoint. When she accuses him of working for HR, Fusco explains that he’s working undercover and made some mistakes, and he’s trying to turn things around. Carter doesn’t believe him and Fusco tells her that he’s working with Reese and Finch. He describes Finch and explains that he was talking to him when she came in. Finch calls and says that he can explain later to both of them, but right now Reese needs their help. Carter wonders who the mole is and Fusco says that he knows everyone in HR and they’ll take them down once Reese has escaped.
Reese and Caroline get to the parking sublevel and head for the service tunnel. However, he spots HR’s car and equips himself with the extra weapons they have in the trunk.
As the sun rises, Finch arrives at the water plant and tells Reese that he’s in position. Reese tells Caroline to go on ahead while he holds Simmons and his killers off. They exchange shots while Alicia gets in the car with Finch and aims a gun at him. She reminds him that they’ve met before and tells Finch that he’s going to help her shut down the Machine.
Reese tries to hold off his attackers but runs out of ammo. However, Fusco and Carter arrive in a car and open fire, giving Reese time to get in with them so they get out. The killers drive away and Carter drives after them.
Alicia tells Finch that before the Machine killed Nathan, Finch’s partner was troubled by the ethics of the situation and the power of the Machine. She’s tired of running from it when there’s no escape, and Finch admits that he’s made some mistakes. However, he insists that the Machine wasn’t one of them, and the Machine didn’t kill Nathan. He explains that she’s been running from the people that have the Machine, people that they trusted, and she tells him that he’s right and she’s lucky that she found Finch first.
As they follow Jablonski and his men, Fusco and Carter both want to know why Reese didn’t trust them. He points out that they were both after him at one point, and then tells Carter to slow down. He then triggers the explosives he rigged in the back of Jablonski’s car, blowing it up. Reese offers to buy them a drink sometime, gets out, and walks away.
Zoe breaks into Caroline’s office and finds the photo of a man on her desk. However, she discovers that it’s a fake and then checks the woman’s computer.
Alicia warns Finch that it could create chaos if the wrong person learned that Finch had access. He points out that she hired Simmons to send men after him because she knew about the irrelevant list, but Alicia admits that she had no idea it existed. Caroline arrives, shoots Alicia dead, and gets in the car behind Finch. Caroline introduces herself as Root, the hacker that went up against Finch and Reese months ago. Zoe calls to tell Reese that Caroline isn’t who they thought, and she’s the one who paid HR. She staged the entire thing to lure Finch out into the open, and now they have a lot to talk about.
Reese goes to the water plant and finds Alicia’s corpse... and no sign of Finch.
Brennan searches the parking garage and receives an anonymous email with the evidence against the heads of HR.
At the police station, Fusco smiles in satisfaction after sending the email and Carter briefly smiles back.
Sagan is revealed as the mole.
Simmons goes to his car, free and clear.
Reese goes to the library but finds no sign of Finch. He takes to the streets and looks up at a camera, and then addresses the Machine directly. He tells it that Finch is in danger because he worked for it, and it’s going to help him get it back. After a moment, a nearby pay phone rings and Reese answers it.