Two men worry about where a kid they hired is. While they worry that he's reckless, a car crashes on a city street at night.
Reese arrives at the library and discovers that Finch is away from his desk. He notices a book nearby and thumbs through it, and a photo of Finch and another man falls out, with the words "In the beginning—N.I." on the back. Finch calls Reese back and tells him they have four numbers: Claire Ryan, a 42-year-old lecturer; Matt Duggan, 33, a waiter; Wendy McNally, 29, a hairstylist; and Paula Vasquez, 23, unemployed. He figures that there is some connection and Reese wonders if one of them could be trying to kill the other three. Finch notes that Claire's number came up first by a millisecond and gives Reese her address, and then warns him to be careful what he looks for or he might find it.
Internal Affairs talks to Carter and points out that there are some holes in her statements. They wonder where the unknown shooter came from that shot Bottle Cap, and why he's interested in protecting Carter. She insists that she has no idea even though it's the man who she has been chasing for the last three months. They don't believe that the man would protect her if she's chasing him, and suggests that she's working with him. They ask if the man has spoken to Carter and she tells them that they have her statement and she won't talk to them again until her delegate is present.
Carter sits down at her desk and Fusco comes over and tells her that she should take some time off. He then asks about the inquiry and Carter says that she's behind a desk and Fusco is working with Olson for now. Fusco asks if she got a good look at his face. Carter says that she didn't, and that she still plans to arrest her guardian angel. Her partner assures her that he has her back and leaves.
Reese arrives at Claire's apartment and discovers the police are already there. Posing as a CSU tech, Reese bluffs his way in and discovers that Claire is already dead and the Machine was wrong.
A man approaches the car crash. A car stops nearby and the license plate belongs to Claire.
Reese grabs Claire's cell phone and downloads her email onto a thumb drive. Fusco arrives with his partner, Olson, and Reese slips away. The detectives confirm that she was beaten and then shot, and that she recently bought a lot of new items. Fusco spots Reese, who motions to him to meet him outside. While Reese waits, he tells Finch to get out on the street to help him cover the remaining three numbers. Finch reluctantly agrees and heads out to check Matt, while Reese watches Wendy and Fusco handles Paula. Fusco comes out and wonders if Reese killed Claire. Reese tells him to watch Paula and says that she's connected to Claire's death.
Captain Womack calls Carter into his office. A man in a suit is going through her file on the mystery man and Womack accuses her of letting him run. The man asks if Reese shot Bottle Cap and Womack forces her to answer. When Carter admits that Reese did, Womack dismisses her.
Reese goes to Wendy's salon and sees a motorcyclist park outside. He goes in after the man, who drops off an envelope and leaves. Wendy notices Reese and asks what he wants. Unable to explain why he was really there, Reese asks for a haircut. She leads him off and asks if he's single, and refuses to let him out on the street.
Fusco watches Paula meet with two men at a construction site. She pays for a package but then spots Fusco and takes off. He goes after her on foot but loses her when she goes around the corner.
Finch takes a taxi to follow Matt, who has quit his job and gone shopping for a motorcycle. Matt tells the salesman that he received a chunk of change when his aunt in Boston died. Reese has Finch to see if anyone is watching Matt, but Finch doesn't see anyone. Fusco then calls Reese and says that he lost Paula, and he figures that she bought a gun. Reese notices that Wendy has left, and an assistant tells him that she had an emergency. Finch tells Reese that Matt is leaving the showroom after placing a deposit, and notices that someone left a baby stroller near the car. He spots the mother nearby and realizes that she's prepared to trigger a bomb. Finch tries to warn Matt but the bomb goes off, knocking him to the ground and killing Matt.
Claire and Matt search the crashed car and find cocaine.
Back at the library, Finch blames himself for not spotting the killer quickly enough. Reese tells him to focus on saving Paula and Wendy, and Finch admits that he can't find any connections. His partner is checking Wi-Fi hotspots and plot where Matt, Wendy, and Claire were. The computers come up with an address on Roosevelt Drive at 11:57 p.m. for four minutes. There was a traffic crash that night, and the victim's name is redacted. Paula doesn't have a phone and Reese figure that she might be a killer. Finch gives Reese the address of Wendy's mother and he hangs up.
At the station the next day, Carter is going over Fusco's case and confirms that Claire's prints were on the car. She confirms that Matt was also there and the CSU figures they were witnesses. They figure that there was money in the car and Claire and Matt took it. Carter confirms that Congressman Hallen's son Jamie was the driver who died, and Hallen was able to cover it up because he's a friend of the police unions. Jamie was speeding and on coke, but the only thing in the car was a brochure for a Haitian children's charity. Carter wants to check out the security footage, but Olson reminds her that Womack told her to stay at her desk. When Carter looks around, she sees the unnamed man from Womack's office watching her.
As Reese goes to see Wendy's mother, Fusco calls to tell him about Hallen's connection. Reese tells Fusco that they know about the crash and asks how Carter is doing. Finch says that they'll keep an eye on her and that Fusco should keep his phone on when he talks to Congressman Hallen so that he can listen in.
Olson and Fusco go to see Congressman Hallen, who wonders why they are there. They ask where Jamie was and the congressman says that Jamie was at a party at the house of Davis Bannerman. Hallen is investigating Bannerman's bank and didn't like it that his son was socializing with the banker. The congressman asks if they can let it drop, but Fusco says that two other people have died because drugs are involved. Hallen admits that Jamie was dealing and warns that they shouldn't believe what Bannerman says. Fusco notices brochures for the Haitian charity and confirms that Jamie set it up. Meanwhile, Finch tries to work out where Jamie was going after he left Bannerman's party, since the crash site wasn't on the way to the boy's home.
Reese approaches the home of Wendy's mother and spots Wendy on the phone. He also sees Paula in the house with a gun and prepares to shoot her. However, Paula hugs Wendy and he realizes that they know each other. He goes inside as Paula gives her sister a new phone and warns that people are looking for them. She threatens to shoot Reese but he easily disarms her, and they explain that they're foster sisters. Reese tells them that he knows about the money, but they're interrupted when a man knocks at the door. The man identifies himself as Dayne and says that his car broke down and his phone died. Reese tells Paula to let him in and then slams his hand in the door as he goes for a gun. Paula and Wendy escape the house out the back while Reese takes out Dayne. However, Dayne's partner opens fire from their car and Dayne uses the distraction to escape.
At the station, Carter shows Fusco the footage of Jamie's crash. It shows that two cars stopped after the crash. One belonged to Claire, the other to Matt. Two other women arrived but the resolution isn't good enough for facial recognition. However, they can see the four people remove a suitcase from the car. Detective Foster at the 82nd precinct is also investigating the crash. The camera also shows a man pull up 30 minutes later in a car with no plates, check out the crash, and make a call. Fusco suggest that Carter talk to Foster and see if he knows anything.
Reese searches the house and finds a letter sent to Susan McNally from St. George's Hospital. He has Finch check on Susan and explains that Wendy and Paula are sisters. Finch confirms that Susan broke her hip recently, and that the bank has foreclosed on the house. He tells Reese to keep the girls safe while he determines where Jamie's money came from.
Carter leaves the 82nd and calls Fusco to tell him that there is no Detective Foster. Someone used a fake ID to gain access to the camera footage. She then turns and confronts the man from Womack's office, Mark Snow, who is following her. He says that he's worried about her and suggests that they go somewhere private to talk. Snow and his partner met with Carter at a restaurant and she realizes that they're CIA. He warns Carter that Reese is dangerous and says that he was his best friend. They explain that Reese used to kill for his country, but now he's killing whoever he wants, some good, some bad. Snow warns that Reese has been destroyed by the things that he was made to do, and his paranoia makes it impossible to trust anyone. Reese's handler was Kara Stanton, but Reese killed her and faked his death. They want to bring Reese in before he kills himself or anyone else, and figures that they can use Reese's trust of Carter to capture him.
At the station, Olson and Fusco meet with Bannerman. Bannerman says that Jamie was stoned and he asked the boy to leave, and doesn't know if he was dealing drugs. The banker says that he had heard that Jamie was dealing with some people that he shouldn't. Afterward, Fusco talks to Finch and warns that Bannerman's story and Hallen's match exactly. The detective figures that Jamie was working as a go-between for the two men and now they're covering up his death.
Reese goes to St. George and spots Wendy. Finch tells him that he knows Jamie was going to LaGuardia Airport to fly to the Cayman Islands on Bannerman's private jet. He signs off so he can check on the Haitian charity, and Reese talks to Wendy. She apologizes for lying to him before and says that Paula is getting food. Wendy then explains that they were out walking when the car crashed nearby. Jamie was already dead, covered in coke, with a suitcase containing a million dollars. The four witnesses divided up the money, $250,000 each, even though they knew it was wrong. Wendy and Paula's share of the money is beneath her mother's bed.
Elsewhere in the hospital, Dayne knocks out Paula and puts her in a wheelchair.
Wendy says that they want to give the money back but don't know who the guys are that are after them. She figures they'll find some other way to save their mother's house. Dayne calls on Paula's phone and tells her to bring the money to the parking garage and exchange it for Paula.
Dayne checks Jamie's car, confirms that the money's gone, and goes to check the cameras.
Finch goes to see Hallen, posing as a blog reporter. He warns the congressman that his enemies plan to use Jamie to bring down Hallen, and explains that there's $30 million in the charity account that has never been spent on Haitian children. Finch explains that Bannerman is setting Hallen up and plans to discredit him by tying him to the funds. Hallen confirms that Finch hasn't gone to the police, and Finch suggests that he close the charity account and donate the money to the Red Cross, eliminating the evidence. The congressman agrees and gets Finch's number on his business pen.
Outside in his car, Finch listens in via the camera in the business pen as Hallen calls Bannerman and tells him that Finch knows about the Cayman charity. Bannerman assures the congressman that he has everything under control and will soon have the money back. Finch sends a recording of the conversation to Fusco.
Reese calls Carter and she asks him to come in and explain some things. He refuses but says that the people who killed Claire and Matt are at St. George in the parking garage. As Reese hangs up, Carter thanks him for saving her life. Wendy gets the money and goes to the parking garage with Reese. Meanwhile, Carter considers her phone and finally calls Snow and tells him that she knows where Reese will be.
Reese sets up with a sniper rifle and tells Wendy to call Dayne and demand to see Paula. Dayne brings the woman out and Reese tells Wendy to meet the exchange. However, a nurse approaches Reese, one who saw him earlier, and asks if he's okay. Reese hides the rifle and assures her that he's fine, but she draws a gun and shoots at him. Reese ducks for cover, tells Wendy and Paula to run, and shoots a steam pipe near Dayne. While the killer is distracted, Reese attacks the fake nurse and knocks her out. When Dayne comes after him, Reese shoots him down. He makes sure that Paula and Wendy are okay, and tells them to keep the money because they earned it and no one will come after them anymore.
Finch checks on the camera in the station and learns that she made a call betraying Reese.
Snow and his men cut off the cameras in the hospital parking garage and the area outside. As Reese goes to his car on the top floor, Snow and Carter pull up. Snow greets Reese, who knows who he is. He tells Reese that the slate has been wiped clean and it's time for him to come home. Reese tells him that it'll never happen, and Snow's aide opens fire with a sniper rifle. He hits Reese in the stomach, and Reese fires, taking out the headlights on Snow's vehicle. He then crawls away in the darkness. Snow realizes that Carter has slipped away and drives.
Finch contacts Reese, who says that it's not looking good. He thanks Finch for giving him a second chance and tells him to stay away rather than risk himself. Finch keeps driving.
Carter comes down the stairs, following the trail of blood. Meanwhile, Finch pulls into the parking garage and gets Reese into the car. Carter comes out and tells them at gunpoint to stop. She recognizes Finch and tells him to get Reese out of there. She helps get Reese into the car and tells them to go.