After the shootout with the CIA, Finch takes the injured Reese to the city morgue. He then bribes the technician, an accomplished surgeon in his own country who can't afford a U.S. doctor's license, to treat Reese with no questions asked.
Carter is leaving home for work when she spots a CIA panel truck watching her and men on the streets dogging her footsteps. She goes up to the truck and pounds on it, and CIA agent Snow comes over and asks if she has a problem. Carter figures that he's being obvious about following her to make a point and tells Snow that it's unnecessary. However, Snow figures that she helped Reese escapes and plans to follow her. He warns her that he'll be checking her professional and personal life carefully and could turn up anything.
At the station, Carter notices that Lionel is away from his desk and checks his files. She finds the surveillance photo of Finch from the evidence lockup and realizes that he was the man who helped Reese escape. There's a number and as Lionel comes in, Carter calls and discovers that it's been disconnected. She tells her partner that she's trying to locate Finch.
Finch poses as a jogger by the river and listens via hidden mike as his partner Nathan Ingram meets with Alicia Corwin, the NSA operative who is the liaison with the government. Alicia demands a status report on the success of the Machine, warning Nathan that if Congress finds out about the surveillance device then they could all go to jail. Nathan gives her a piece of paper with a Social Security number and tells her to check it out. Once she leaves, Nathan meets with Finch, who assures him that the number came from the Machine and it's what they need to soothe the government.
Finch finds an apartment for a wheelchair-bound Reese to stay in while he recuperates from his wounds. The super, Ernie Trask, shows Reese around the apartment and talks constantly about how he used to be a rich man in Miami. Once Trask leaves, Finch arrives and makes sure that Reese is comfortable. When Reese wonders about Carter, Finch assures him that Snow is busy with her. Reese tells him to keep an eye on Carter and then realizes that Finch picked the apartment building because they have a case. Finch admits that he did and tells his partner that the new number is for Trask.
Finch and Reese watch Trask working in the courtyard and chatting with the tenants, including a young cook, Lily Thornton. They've already done a background check and confirmed that Trask grew up in a small town and has been the super at the building for the last 14 years. Finch has hacked Trask's cell phone and confirmed that in the last week he has visited three pawnshops and probably purchased a gun.
Snow meets with his partner, Tyrell, who admits that he hasn't been able to find Reese. When his superior complains that Reese is still alive, Tyrell points out that the goal was to capture Reese, not kill him. Snow isn't so sure and asks about Carter, and Tyrell confirms that no one has contacted her.
Finch hacks into the building's wireless network and accesses the tenants' webcams. They check the cameras and spot Doug Stanley, the building's security guard, who is investigating several jewelry thefts from tenants. Reese sends Finch to the basement and then breaks the apartment sink. When Trask comes up to fix it, Finch sneaks into his office/apartment, plants hidden cameras, and searches for the gun. All he finds is bullet, but he figures that's enough.
Trask starts to repair the sink but then goes back to his office for the correct wrench. As Reese warns Finch, Finch finds photos of Lily hidden in the office. He gets out into the hallway just as Trask arrives, and the super figures that something is going on. Finch gets into the elevator just in time, and Reese warns him in time to get out as Trask shuts down the power. As Finch heads back to the apartment, he runs into Doug, who is getting a call from Trask accusing Finch of being the robber. Reese checks the webcams and confirms that Doug is the jewel thief. He relays the footage to Finch, who uses it to blackmail Doug into letting him in go in return for his silence.
Finch runs into Nathan’s office, plugs a flash drive into his friend’s laptop, and then tosses coffee onto the keyboard. Alicia and her superior, NSA Deputy Director Denton L. Weeks, barge in a few seconds later and Finch sits down and pretends to be from IT repairing the laptop. The newcomers turn to Nathan and tell him that the 9-digit number was the Social Security number of a man named Kurzweil, who was selling secrets to the Iranian. They didn’t suspect him until they traced the SSN and put a tail on him, and saw him meeting with his Iranian contacts. Weeks wants to know how the Machine did it, but Weeks says that it’s a black box and that there is no way to see the software. When the deputy director objects, Nathan explains that it was deliberately designed that way so that there would be no potential Fourth Amendment violation. Weeks threatens to stop payment to Nathan’s company since they’re a private contractor, but Alicia is forced to tell him that as a matter of patriotism, Nathan is only charging $1 for the Machine. Meanwhile, Finch listens in while accessing the Machine, and it warns him that Weeks is a potential thread.
Reese makes a bump key for Finch so he can get into any apartment in the building. He then brings up information on the woman in the photo, Lily, and confirms that she’s a chief chef at a Manhattan bistro. The newspapers have romantically linked her to Rick Morris, a powerful restaurateur. They check her wifi and confirm that Lily keeps changing her password, and figure that she’s protecting herself from Trask. Reese wants to follow her but Finch points out that he’s in a wheelchair and will do it himself. Concerned, Reese shows Finch how to defend himself with the basic tactic of poking Trask in the eye if he comes after him.
Finch then goes to Lily’s apartment and plans to put a hidden camera in her air vent. However, he realizes that there is already a camera there and confirms that it’s streaming to a hidden network. Finch pulls it out, figuring that Trask planted it.
Carter’s request for a cell phone log comes in and Lionel catches a glimpse of it before she grabs it. The officer then walks down the street and spots the two CIA men following her. She goes into a hotel lobby and manages to give them the slip, taking a taxi.
Finch is at Lily’s restaurant watching her and calls Lionel. Lionel tells him that Carter is trying to track Finch by his phone number, but Finch sends him a package containing a medicine bottle. He tells Lionel to drive to Connecticut and draw the CIA agents away. After hanging up, Finch checks with Reese, who is checking on Trask’s emails and trying to hack the hidden wifi network. Reese has also checked Trask’s background and discovered that the super’s wife disappeared 13 years ago, and that Trask claimed she went to live with her relatives in Boca Raton. Finch watches as a deliveryman brings Lily rose which she promptly throws away. When he hears the news, Reese checks the courtyard and sees Trask working near a rose garden.
Carter uses the phone log to track the phone booth where Finch supposedly called her. He calls the booth and tells her that he altered the log earlier that day. He asks if she still wants Reese and Carter says that she wants to know what they’re doing if she’s going to lie to the CIA for them. Finch tells to look around and Carter realizes that he’s sitting at a nearby diner. She goes in to confront him and Finch talks about how his father and brothers threw him into the pool when he was 9 to see if he could swim. Carter doesn’t understand what he’s talking about, and Finch points out a man named Derek Watson who is sitting at the counter. He explains that Derek lost his job, his house, and his wife, and that he’s going to be involved in a violent crime. Finch asks Carter if she brought her service weapon and then walks away. Carter calls in and confirms that Derek has a clean criminal record, and then follows him as he goes to Truprime Mortgage. Derek’s file shows that Truprime was the company that foreclosed on Derek’s house, and that the man Derek is now following, John Dalton, was the man responsible.
The two men who followed Carter report to Snow that they lost her. Disgusted, Snow sends them out and tells Tyrell to expand their search to anyone who rented an apartment or hotel room since the shooting.
Finch follows Lily back to the apartment building, while Reese checks and sees Trask digging a man-sized hole in the courtyard. Going back over the recordings, Reese sees Trask loading a gun and warns Finch. As Rick enters the building, Trask tells him to stay away from Lily. With Finch following Lily, Reese has to handle the situation himself. Using his crutch and a gas-soaked cloth, he sets off the fire alarm as Trask starts to draw his gun. The tenants evacuate the building and Trask hastily puts away his gun. Reese tells Finch what happened and his partner suggests more aggressive tactics. He checks Lily’s text messages and sees that Trask sent her one demanding that they talk. Finch figures that they need to get Trask out of the building for good.
When Trask returns to his basement office, he finds Reese waiting for him. Reese points a gun at him and tells Trask that he knows all about the roses and the text, and that the super will be leaving for good. Trask tells Reese that he doesn’t understand and that Rick isn’t Lily’s boyfriend. Reese repeats his threat and Trask tells him that he cares about Lily but he isn’t stalking her.
Finch comes back to the apartment and manages to decrypt the wireless network, discovering who created it. Reese calls to tell him that Trask got the photos from a tenant’s apartment. Finch checks the monitors and sees Rick go into Lily’s apartment, and they realize who has really been stalking Lily.
An angry Rick demands to know why Lily is blowing him off after they went on a date, and she points out that they just happened to meet at the same party. He promises to help her career if she dates him and figures that she warned Trask, and then shoves her into the wall. Finch arrives just in time and pokes him in the eye, and then gets Lily out. Trask and Reese get there and Rick stabs Trask with a letter opener. Reese attacks the stalker with his crutch until Rick finally charges at him, misses, and goes out the window.
Tyrell tells Snow that they’ve found a bottle with Reese’s prints in Connecticut at a veterinarian’s office. Satisfied, Snow recalls his men and they head for Connecticut.
The police arrive at the building and get Lily’s story of what happened. Meanwhile, Doug is arrested when Finch calls in an anonymous tip that he’s the jewel thief. Meanwhile, Finch meets with Reese and tells him that he checked Trask’s backstory, and it turned out that everything he said was true. Trask used to be a drug dealer in Miami until he turned state’s evidence and went into witness protection. His wife left him and went to Boca Raton to stay with his wife. Reese, surprised, suspects that Finch is the one providing all of the information and that there is no Machine.
Finch and Nathan share a toast to the success of the Machine and Nathan handling the NSA. Nathan is curious as to how the Machine found the number and finch walks his partner through the process that the Machine used to stitch together a series of receipts and security photos to locate where Kurzweil met his Iranian contacts. Nathan is concerned that the Machine could fall into the wrong hands and Finch assures him that when he’s done, he’ll have thoroughly coded the Machine so that no one can access it. He’s well aware that Weeks has been trying to tap into the Machine through the government feeds, and explains to Nathan that the Machine itself warned him about Weeks’ attempts. As they leave, Nathan comments that Finch talks about the Machine as if it were alive. They’re both unaware that the Machine has identified Nathan as a potential threat.