The CIA operatives cut the cameras, confront Reese on the parking garage, and shoot him.
Finch takes the wounded Reese to the city morgue and tells the coroner that he knows he's Farouk Madani, a surgeon from Naraj who can't afford a license because he sends all of his money home to his family. He then pours money from a bag in front of Farouk and offers him all of it to tend to Reese's wounds, no questions asked. Farouk immediately goes to work on Reese.
The next day, Carter leaves home and spots a green panel truck parked across the street. Men are watching her and Carter goes to the truck and orders everyone out. Snow comes up and asks if there's a problem, and then asks if she's going to be out for a while. Carter figures that he's making a point by revealing himself and tells him that it's unnecessary, but Snow openly admits that he suspects her of helping Reese escape. As Carter walks away, Snow warns her that he could turn up anything in his investigation of her, and it could ruin her career.
Carter arrives at work and notices that Lionel is away from his desk. She goes to his computer and finds the paper that he wrote his password on. She accesses his computer and discovers that he has footage on Finch from when he was at the evidence locker, including a phone number. As she calls the number and discovers that it's disconnected, Lionel arrives and Carter tells him that she's trying to trace Finch.
In 2005, Finch jogs to the park and listens in as his partner Nathan Ingram meets with Alicia, their representative in Washington. She wants to know what his company has been doing with the NSA feeds that he's received, and warns that he would go to jail if the public found out. Alicia demands progress and Ingram gives her a piece of paper with nine digits and tells her to figure it out. Afterward, Ingram meets with Finch and complains that he always has to be the public face of the company. Finch assures him that the number will pan out because the Machine provided them.
The CIA continues to access CCTVs to find Reese. Meanwhile, a wheelchair-bound Reese checks into an apartment. The super, Ernie Trask, tells him that he's there for him. He tries to make small talk, going on about how he used to be a rich man in Miami, but Reese refuses to chat. Once Trask leaves, Finch comes in and makes sure that Reese is comfortable. He tells Reese that Snow is preoccupied with Carter, and Reese asks Finch to keep an eye on Carter. However, Reese realizes that Finch got the apartment for a reason: the Machine has given them Trask's number.
Trask is outside chatting with the guests, including a cook, Lily, while Finch tells Reese that the super comes from a small town and has been at the apartment for the last 14 years. There are 241 people in the building, but Finch has hacked Trask's phone call log and discovered that he's visited three pawnshops that sell off-the-book guns.
Snow returns to the truck and meets with his partner, Tyrell. Tyrell notes that Snow told him to try and wound Reese rather than kill, and confirms that Carter hasn't contacted anyone.
Once he makes sure that Reese is comfortable, Finch hacks the apartment's wireless system and accesses everyone's webcams. Reese spots Doug Stanley, the building's security guard, who is investigating some jewel thefts. The two men find nothing conclusive and Reese says that Finch will have to do some legwork. Finch goes to the basement while Reese breaks his sink and then calls Trask. Once Trask leaves his basement office, Finch breaks in, plants cameras, and searches for a gun. He doesn't find one, but he does find bullets.
Trask realizes he has the wrong wrench and goes back downstairs. Reese warns Finch, who finds photos of Lily. Finch then comes out just as Trask comes down the stairs. The super realizes that Finch was in his apartment, but Finch gets into the elevator before the super can stop him. Reese checks on the camera and warns Finch that Trask is shutting down the elevator. Finch gets out just in time and Reese directs him back to the apartment. However, Finch runs into Doug as he emerges from a woman's apartment. Trask calls Doug and gives him Finch's description, while Reese checks the cameras of the women's apartment and confirms that he's the thief. Finch shows him the footage via his iTouch and tells Doug that he'll erase it if Doug forgets him. Doug agrees and walks off.
Finch runs to the office, plugs a flash drive into Ingram's laptop, and tosses coffee on the computer. Alicia comes in seconds later and apologizes for the interruption, and then introduces her superior, Deputy Director Denton L. Weeks. Weeks explains that the number Ingram gave him earlier was the Social Security number of a man named Kurzweil, and it turned out that Kurzweil was a traitor. When Weeks demands an explanation, Nathan explains that they can't access the software and that it watches for threats at all times. Further, if no one sees the Machine's programming, no one can violate the Fourth Amendment. Weeks and Alicia are unhappy that they don't get anything more than a number, but Ingram insists that is how the Machine works. When Weeks threatens to cut payment to the company, Alicia informs Weeks that Nathan built the Machine for $1. Meanwhile, Finch monitors the entire conversation through the Machine and it tells him that Weeks is a threat.
Lily is in her apartment, complaining that a man is always watching her.
Reese provides Finch with a bump key to get through every door in the apartment. He's also brought up info on Lily Thornton, a rising star at a top Manhattan bistro. She's linked to Rick Morris, a powerful restaurateur. Lily changes her wifi password every day, making it impossible for them or Trask to access her computer or camera. Reese tells Finch that he'll follow her despite the wheelchair. When Finch points out that it's a mistake, Reese admits that he's feeling restless. He insists on giving Finch a basic self-defense lesson which consists of poking someone in the eye.
Finch goes to Lily's apartment and plants a camera in the vent. However, he discovers that there is already a camera there, streaming to a hidden network. Finch figures that Trask is responsible and yanks out the camera.
Lionel gets the cell phone log that Carter requested. She grabs it and leaves, well aware that the CIA is still following her. She walks down the street, goes into a building, and requisitions a man's jacket. When the two agents come in, Carter slips out through another door and takes a taxi.
Back at the station, Lionel receives a call from Finch, who is at Lily's restaurant. He warns him that Carter is tracking Finch but admits that he doesn't know why. Finch has sent Lionel a medicine bottle with Reese's fingerprints on it and suggests that he drive to Connecticut and plant the bottle, leading the CIA off. Once he hangs up, Finch keeps an eye on Lily, while Reese tells him that he's still working on Trask's emails. He's also trying to break into the hidden wireless network without success, but has found out that Trask used to be married. His wife disappeared 13 years ago and Trask never called the cops. A deliveryman brings in a bouquet of roses and she has a co-worker throw them away. Finch figures that she knows about her stalker, and Reese realizes that Trask is growing roses in the courtyard.
Carter goes to the phone booth where Finch supposedly made his call. He calls and says that he altered the location logs that morning and asks if she still wants Reese. Carter explains that she wants to know what they do if she's going to continue lying to the CIA. Finch tells her to turn around and she realizes that he's sitting in a nearby diner. Carter goes in and demands answers, and Finch tells her about how he was tossed into the deep end of the pool when he was 9 so he could learn how to swim. He then points out a man at the counter, Derek Watson, and explains that he lost his job, ran out of money, and lost his house and then his wife. Finch says that now Derek is about to be involved in a violent crime. When Carter points out that Finch can't know that, he asks if she brought her service weapon. Finch walks away and Carter calls Lionel and has him do a trace on Derek. The information matches what Finch told her, and there's no criminal record on him. Carter notices that Derek has gone to Truprime Mortgage, the company that foreclosed on his house. The man responsible, John Dalton, comes out of the office and Derek follows him while Carter follows Derek.
Snow's men report that they lost Carter. He sends them back out and then tells Tyrell to expand the search to all hotel rooms and apartments rented in the last few days.
Finch follows Lily home and checks with Reese. Reese figures that Trask is going after Rick, not Lily, and is now digging a man-sized hole in the courtyard. Checking the cameras, Reese sees Trask loading his gun and warns Finch.
As Rick comes home, Trask confronts him and tells him to stay away from Lily, insisting that she doesn't love him. Finch is five minutes away and Reese has no choice but to deal with the situation himself. He wraps a cloth around his crutch, sets it on fire, and sets off the alarm just as Trask goes for his gun. The other residents come out and Trask has no choice but to back off.
When Lily comes home, she discovers that things have been moved in her apartment.
Reese warns Finch that it isn't over and Finch suggest more aggressive tactics. He's cloned Lily's call log and sees her receiving text messages from Trask demanding that they talk. Finch insists that they get Trask out of the building.
Trask comes home and finds Reese waiting for him. Reese draws a gun and tells the super that he'll be leaving and says that knows all about the roses and the texts. Trask says that Rick isn't her boyfriend and Reese doesn't understand, but Reese tells him to get out and never come back. Undeterred, the super says that he cares about Lily but not like that.
Finch arrives at the apartment and decrypts the wireless network. He realizes that Trask isn't the stalker just as Reese calls to tell him that Trask explained that he got the photos from a resident's apartment. Meanwhile, Rick enters Lily's apartment and moves threateningly toward her. Finch sees him and tells Reese that they need help.
Lily tells Rick that he needs to back off, and they just happened to be at the same party. Rick insists that he can help her career and wonders if she told Trask about them. He grows angry and shoves her against the wall, and Finch comes in and pokes him in the eye. He gets Lily out while Trask arrives and tries to stop Rick. Rick stabs him with a letter opener but Reese arrives and uses his crutch to hold off Rick. Rick finally charges at him and Reese throws him out the window where he plummets to the ground.
Tyrell tells Snow that they've found a bottle with Reese's prints at a veterinarian's office in Connecticut and they head off.
The police arrive and Lily tells them what happened. Meanwhile, Finch calls in an anonymous tip about Doug and his theft of the jewelry. Reese gives Finch Trask's gun and Finch explains that all of Trask's stories about Florida were true. He testified against the Miami mob and went into witness protection, and his wife left him as a result. Reese wonders how Finch found out everything and suspects that there is no Machine.
Carter follows Derek and Dalton to a restaurant. Derek draws a gun on Dalton but Carter steps forward and disarms him. As she handcuffs him, Finch calls and tells her that's what they do.
Ingram and Finch share a bottle of champagne in their office and toast to their success handling the government. When Ingram asks how the Machine came up with the number, Finch reveals that 18 gas station receipts from the same gas station came up. There was a SUV present during most of the visits, a SUV registered to the Iranians that Kurzweil was dealing with. Ingram notes that the Machine's ability is terrifying, and Finch assures him that when he's done, the Machine will be so well coded that no OS can crack it. He is convinced that the government would abuse the Machine if they can access it, and reveals that Weeks has been trying to access the Machine through the NSA feeds. Finch vows to make sure that no one else gets hold of the Machine, and that it was the one that warned him about Weeks. As they leave for the night, Ingram comments that Finch talks about the Machine as if it's alive.
Somewhere in the Machine's programming, Nathan Ingram is identified as a potential threat.