A businessman, Bill, is carrying flowers and gets into an elevator with two men. As the doors start to close, Reese gets in the elevator with Bill and points out that his wife prefers flowers. When Bill asks if he works there, Reese explains that he's an independent contractor and advises him against stepping out on his wife. He then explains that Bill's wife hired a couple of men to come the office, disable the surveillance cameras in the elevator, kill Bill, and make it look like a robbery go wrong. The two other men go for their guns. When the elevator stops at the bottom, Reese steps out and tells Bill to call the police and a good divorce lawyer.
A man gets a call and is informed it's high priority and will pay triple the normal fee.
Later, Reese calls Finch from across the street and tells him that he saved Bill. Finch advises him to get some rest but Reese says that he needs to do some research. When Reese wonders if he has another Number, Finch says that it's an unusual case. He slips away from Reese and says that they'll meet on his terms.
Detective Carter arrives at the elevator shootout and gets the story that Bill reported that a guy in a suit intervened.
Reese meets with Finch at a cemetery and admits that his research didn't go well. Theresa Whitaker, 15 years old, is the next Number. She's had disciplinary problems but is basically a good kid. When Reese wonders where she is, Finch points out Theresa's headstone and explains that she was murdered two years ago along with the rest of her family.
Finch's partner Ingram meets with the programmer as he exercises next to the Machine that he is designing for the government. Ingram has yet another reward that he's accepted for both of them, and complains that he's exhausted from all the PR work that he's done. He notices the government feed with all the data, and Finch explains that he's completed the program to gather the information, and now he has program the Machine to find terrorists by filtering through the data. He warns that it will take another four to five years to complete the work.
Finch and Reese meet at the dock and Finch explains that Theresa was last seen there two years ago. Her father Grant took the family for a weekend sail and no one came home. Only the bodies of Grant, his wife Elizabeth, and their 18-year old son were seen. Grant was a real estate developer and the police theory is that he shot his wife and kids and then himself after the market crashed. Reese wonders why she hasn't turned up and figures that she's dead, but Finch insists that the Machine is right and that Theresa is in danger.
Reese slips into police headquarters using Stills' badge and grabs Fusco. He tells Fusco that he needs a file, but Fusco warns that IAD is onto him and he is close to being put away as a dirty cop. Reese isn't interested and tells him to get the file on the Whitaker case.
At the library, Reese goes over the files and confirms that the evidence indicates it was a professional hit. He admits that he doesn't know why the killer disposed of Theresa as well, and Finch tracks down Theresa's aunt and uncle. Reese wants to talk to Deacon Page, an older boy who was with Theresa when she was picked up for vandalism. He's been arrested multiple times since then and they figure that Theresa might have gone to him as a friend. Reese warns that they don't know how much time they have and that they need a little help.
Finch poses as an insurance agent and goes to see Theresa's aunt, Elizabeth. He claims that she and her husband Derek are listed as next of kin, and Elizabeth says that they divorced a year ago. She's interested to learn if the police have closed the investigation and she had hoped that the body might drift back so they could bury it. Derek never got over it and Elizabeth admits that they haven't spoken since they split. Finch asks if she had any children and Elizabeth quickly says that she didn't. She explains that Theresa was a bright girl and insists that she had bad parents.
At police headquarters, Carter is going over the cases involving Reese and discovers that most of them have been redacted. Her partner Kane finds a missing persons case from 2007 involving her suspect. The Feds have pulled the file and Kane warns that it's above her pay grade.
Finch calls to tell Reese what he's learned and hasn't been able to find Derek. Reese is busying checking skate parks for Deacon and finally tracks him. Posing as a cop, Reese demands to know the last time that Deacon has seen Theresa. While they talk, Reese takes his phone and pairs it with his own. Once Deacon leaves, he sends a message telling Theresa to bolt. Reese looks around and sees a nervous-looking girl taking a cell phone call. She runs off and he goes after her. However, when Reese grabs her, she cuts him with an x-acto knife and gets away.
Finch goes to IFT, the software design company where everyone knows him as Harold. His boss confronts him and tells him that he needs to finish his current project as quickly as possible. When Finch gets to his cubicle, he finds Reese waiting for him. Reese notes that the HR records indicate that Finch has worked there 17 years and has only been promoted twice... and no one knows that he owns the entire company. Finch says that the best place to hide is in plain sight, and that if Reese gives him away, everyone in the department would be assigned or promoted. Reese tells him that Theresa is alive but that he lost her. He's confirmed that she's using a skimmer to capture account numbers and pins from ATM users and sell them online to cover her expenses. Finch says that he can track her down and promises to find Derek, and plans to check Grant's finances. Reese says that he'll find the shooter by seeing where he can hire one. As he leaves, a woman comes over and asks "Harold" who his friend is.
Fusco takes Reese to a seedy bar where a fixer sets up contract killings in return for a percentage. Reese prepares to go in and Fusco warns that people just don't talk to anyone who strolls in. The ex-agent ignores him and goes in. Seconds later, two bounces toss Reese out as Fusco watches. Once the bouncers go inside, Reese smiles at Fusco, goes back inside, and there are gunshots. Reese walks back out and tells Fusco that he has a name.
As Reese arrives at a prison, he calls to tell Finch that the fixer gave him the name of Solnick, a contract killer. Solnick was locked up for a different crime so Reese has come to visit him. They talk and Reese asks him about the Whitakers. When Solnick stays quiet, Reese threatens to tell the brother of a murdered gang leader who killed his sibling. Solnick recognizes Reese as a fellow killer and figures that Reese already knows what happened. Reese asks why he let Theresa alive and Solnick explains that he doesn't kill kids and he's made that clear to the other prisoners. The person who hired him did so anonymously, and Solnick asks Reese who hired him. Afterward, Reese updates Finch and they figure that the person who hired Solnick learned that he doesn't kill kids and spared Theresa. Finch has a lead and confirmed that Grant bought real estate in one deal with a company named Landale.
In the park, a man grabs Deacon and threatens him, and then follows him.
The principal at Landale is a real estate developer named Jimmy Calhoun. Another man comes in and Reese identifies him as Derek. Before he can pursue the matter, Finch gets a report that Theresa tried to sell some ATM numbers online to raise cash. He traces the IP address and sends Reese there, and he confirms it's a wireless address. He spots Theresa in a Laundromat and comes after her, but she draws her knife and tries to hold him off. Reese says that the man who killed her family is in jail and he'll protect her, but the new killer comes up behind him. They struggle and the killer throws Reese out the window and then prepares to shoot Theresa. Reese shoots him and goes after Theresa as she runs and tells her that she needs to trust someone. They're unaware that the killer is wearing a bulletproof vest.
Reese takes Theresa to a hotel room and asks if she knows who targeted her family. She says that she doesn't, but explains that she doesn't trust her uncle. Grant blamed Derek as he was killed. Finch arrives to keep an eye on Theresa while Reese goes to pay a man a visit. As Reese leaves, Finch tells him that Derek's cell phone GPS is active.
As Derek leaves a bar, he gets a call that IDs Grant as the caller. Reese is waiting for him and hustles him into a car.
Elizabeth calls Derek and leaves a message, unaware that the killer is wiretapping her phone.
Reese takes Derek to the docks and explains he knows about how Grant made a deal with Calhoun at Landale for some land that was ruined by an oil spill. Derek insists that he tried to help Grant, but Reese notes that with Grant's death, the land goes into probate and Derek gets it. The brother-in-law explains that Grant thought they'd make money on the land but needed money to buy it, and Derek sent him to Calhoun. Calhoun was laundering money, but when the government didn't pay on the oil spill in time, Calhoun killed Grant and his wife and son to get the money back out. Calhoun didn't kill Derek because he was made the administer of probate, and Derek is supposed to sign the land over in a week. The government did clean the site and now the land is worth 30-40 times what it's work. Theresa is the legal heir to the property, and has spent two years in hiding because Derek didn't come forward to clear her father's name.
At the hotel, Finch talks to Theresa about Elizabeth and how she seems like a lovely person. He tells the girl that Elizabeth misses her and that he knows what it's like to lose someone and feel the need to disappear. However, he says that you don't want to leave people behind.
Finch comes to the Machine room and finds Ingram going over several personnel files. He asks when Finch was going to tell him that he was receiving information on murdered people and didn't do anything, and Finch admits he probably never was going to tell him. The programmer explains that the Machine doesn't understand the difference between relevant terrorist crimes and "irrelevant" violent crimes. There are only eight people in the world that know the Machine exists, and that if anyone else finds out then there would be an uproar. The Machine would be turned off and dozens of terrorist plots would succeed. Ingram wonders how they can live with the knowledge that they're letting people die. Finch says that he's programmed the Machine to delete the irrelevant list every night at midnight, and that they built it to save everybody, not just somebody.
Derek returns home and finds the killer waiting for him in his living room. Meanwhile, Reese calls Finch and brings him up to speed. Finch realizes that Theresa is leaving and goes after her, while Reese follows Calhoun as he goes. Theresa tells Finch that she's better off on his own, but he says that she'll have to trust someone eventually.
The killer tortures Derek and tells him that Calhoun can always hire a couple of lawyers. Derek still refuses to talk and the killer shoots him dead.
Calhoun meets with a councilman and thanks him for his support on some land that will be ready to be rezoned as residential within a month. Reese watches the entire conversation.
Carter and Kane are called to Derek's apartment after the shooting is called in. The killer left a photo of Theresa stuffed in Derek's mouth, and Carter figures they need to identify her and soon.
At the hotel, Theresa calls Elizabeth and the killer intercepts the call. Theresa is unable to say anything to her aunt and hangs up, but the killer tracks the source. He then sends a text message to Calhoun in his limo, notifying him that he's found the girl. As Calhoun hangs up, Reese rams his limo, gets out, and tells the injured Calhoun to call off the killer. When Calhoun tells him that it's too late, Reese calls Finch and tells him to get off the floor. As they get to the elevator, they realize the killer is coming up. They duck back into the room as the killer emerges from the elevator, jams the stairway doors, and knocks out the camera.
Finch watches through the peephole and realizes that the killer is going to turn off the hallway lights. They quickly turn off the room lights but the killer spots them and breaks in to the neighboring room. He hears voices on the other side and breaks in, but discovers that they've called the hotel room on Theresa'' phone and left it as a distraction. Finch and Theresa duck into an access hallway and barricade the door. The killer finds them and Finch sends Theresa down the fire escape. However, she refuses to abandon him. The killer comes round the corner and prepares to shoot them, but Reese arrives just in time to kill him.
Reese calls Carter and says that it's time for a face-to-face meeting. He directs her to a park and she agrees to meet him. She brings a number of plainclothes cops with her and surrounds the park. Carter doesn't see Reese, but she does find Theresa sitting on a park bench. Theresa tells her that her friend said he could trust her, and Carter realizes that she's been set up. As she takes Theresa away, Reese and Finch watch and then go their separate ways.
Calhoun is arrested. Meanwhile, Carter questions Theresa but the girl insists that the trauma caused her to forget anyone who might have helped her. Elizabeth arrives to pick up her niece and the two embrace.
Reese returns to the IFT office and Harold's coworker says that no one is quite sure where he's gone. As she leaves, Finch calls Reese and says that he's a very private person. He insists that he has his reasons to his identity and tells Reese not to call him. Finch then leaves past a statue of Ingram, the company's founder... who died in 2010.