In the middle of the night, a hijacker stops a truck using a flaming wreck. The hijacker takes out the drivers and drives off with the cargo. Soon Peter Yogorov finds out that his heroin was stolen and promises to find out whoever stole from him.
When Reese arrives at the library, Finch tells him that they have thirty-eight Numbers from the Machine. All of them are policemen working for HR, and he figures that some threat is targeting the corrupt organization. Sam arrives while Reese calls Fusco, who tells him about the hijacking. Reese goes to the crime scene posing as a police detective and they talk to the driver. He confirms that HR was responsible for the truck's safety, and they've failed. Reese notices a CCT nearby and tells Fusco to download the footage, and checks in with Finch. Finch figures that Yogorov will demand restitution for HR and set off a war between the two organizations.
Several days earlier, Carter meets with Alonzo and he wonders if she knows what happened between Terney and Laskey that led to them apparently shooting each other. She feigns ignorance and Alonzo figures that it's HR-related. Carter says that she isn't pursuing her suspicions about HR's involvement in Cal's death anymore. Alonzo tells her that Cal would be proud of what she's done and promises that he'll find the people who killed his godson. As they talk, Carter secretly clones his cell phone.
Once Carter leaves, Alonzo calls Simmons and tells him to keep an eye on Carter. When Simmons wonders if he should eliminate Carter, Alonzo says that they can't afford to draw any more attention. Simmons says that he's meeting with Yogorov later to negotiate a deal. When Simmons and his new underling, Detective Stan Mitchell, meet Yogorov and his lieutenant Nikolai at a grain depot, Carter listens in on her clone of Simmons' cellphone. Yogorov isn't interested in paying the extra 10% that HR wants, and complains that HR is treating him like a lackey. He tells Simmons that he'll take his chances without HR protection and walks off. When Mitchell wonders what Simmons wants him to do, his superior says that he has a new assignment for him.
When carter goes home to her apartment that night, she finds Reese waiting for her. He asks if she wants him to take care of the HR man running surveillance across the street, but Carter says that she has it handle. She explains that her son Taylor is somewhere safe and that she wants Reese to stay clear of her investigation because he's still a wanted man. Reese agrees to abide by her decision and tells her to do what she has to, but warns that HR won't go down without a fight. Once Reese leaves, Carter breaks her cellphone so that Finch can't listen in or track her.
In 2005, Carter goes out on the streets for the first time as a cop. She notices her ex-husband Paul Carter across the street and goes over to confront him. Paul says that he just got into town and is getting work with a construction crew, and wants to know what his son is doing. Carter asks if he went to the VA and Paul insists that he doesn't need to. She reminds him that he was suffering from PTSD after the war and that he's not going to see their son again until he goes to the VA for professional help.
Fusco arranges a meeting with Carter and asks how she's doing. He then asks about Terney and Laskey, and suggests that someone made it look like they shot each other. Carter insists that she doesn't want any part of it now, saying that it isn't worth the risk to find out. She advises Fusco to lay low and he leaves. Once he's gone, Carter makes a call and asks the person at the other end to pay a visit.
That night, Yogorov is eating at his favorite restaurant and Nikolai informs him that the shipment is en route as planned. Yogorov discovers a bullet in his food, draws his gun, and runs into the kitchen. Elias is there, cooking at the stove, and Scarface and his men easily capture Yogorov and Nikolai. Yogorov wonders why Elias is still in town, and Elias explains that he wants to make HR suffer for what they did to him. Scarface gives Yogorov a file and Elias tells the Russian mobster to take a look at it. He leaves with his men and then calls Carter and tells her that Yogorov got the package. Carter advises him to lie low for a few days, and Elias wishes her luck. Sam joins Carter at the diner where she's seated and gives her a bag of guns, and Carter thanks her for not telling Finch and Reese. When Sam asks if she can use an assist, Carter says that she'll take it from there.
Later that night, Carter intercepts Yogorov's truck. Wearing a gas mask, she shoots a tear-gas canister into the cab, takes out the two men, and puts a burner phone on the street. She then drives off with Yogorov's cargo of heroin.
Once Fusco downloads the footage from the CCTV, he sends it to Reese and Finch. Finch is sure that none of the thirty-eight Numbers have the skills to pull off that kind of hijacking, and Reese realizes from the hijackers' movements that she's a woman. They suspect Sam, who chooses that moment to come in. When they ask her if she was responsible, Sam admits that she borrowed Reese's guns, and they realize that Carter is the hijacker and out to start a war. Reese tells Sam and Finch to get eyes on all thirty-eight Numbers before one of them goes after Carter.
Alonzo is in his office at city hall when Yogorov calls him. The mobster says that Alonzo's phone number was on the burner phone left at the hijacking, and he accuses Alonzo of ripping him off. Carter is listening in from the roof of a nearby building overlooking Alonzo's office. Alonzo insists that he had nothing to do with the hijacking, but Yogorov tells the deputy mayor that he has a file with information on the entire HR organization. If Alonzo doesn't return the stolen heroin then Yogorov will kill every HR member.
Reese breaks into Carter's apartment and finds the board she's using to track HR. Alonzo is listed as the leader and Reese call Finch to warn him that the deputy mayor is the one who had Cal killed. Meanwhile, Carter is monitoring her apartment by webcam and calls him on his cellphone. Reese warns her that revenge isn't the answer but carter asks him to trust her to do what needs to be done. She hangs up and then aims a sniper rifle at Alonzo, who has called Simmons. Simmons admits that they don't have a lead on the hijacking just as Carter opens fire on Alonzo. She deliberately misses as Alonzo takes cover, and then leaves the roof. Alonzo tells Simmons that Yogorov's people are shooting at him and tells his lieutenant to kill the other mobsters but to bring Yogorov to him.
At the library, Finch discovers The Machine sending him more Numbers... all of Yogorov's men. He figures that HR will win the war in the end because they have the law on their side.
Simmons and his crooked cops pick up all of Yogorov's mobsters and take them to the docks to execute them somewhere private. Nikolai manages to call Yogorov and warn him, just as Carter arrives at Yogorov's apartment. She tells him that he's the last one left and warns him that HR is coming to kill him. She takes out a pair of handcuffs and tells Yogorov to come with her if he wants to live.
In 2005, Carter's babysitter Lisa calls her home. Paul is sitting on the couch with Taylor, and Carter has Lisa take Taylor to his room. Paul insists that Taylor needs him in his life, but Carter says that their son needs a father who can get the help he needs. He refuses, flying into a rage, and Carter goes for her gun. Paul realizes that he's lost it and wonders if she would shoot him, and Carter orders him out. Once he leaves, Carter goes to her son's room and assures Taylor that as long as they have each other, they'll be fine.
Carter takes Yogorov to Bedford and hides him at a sheriff's station, booking him under a false name on a DUI charge. She tell him that she hot at Alonzo and knows that he's the head of HR, and that he had Yogorov and his men kill Cal. Yogorov doesn't see the point but Carter warns him that she has enough to put away him as well as HR. However, she wants Alonzo worse than Yogorov. When Yogorov refuses to turn on his former partner, Carter points out that Alonzo will be coming for him, and that if they can't get to him then they'll go after Yogorov's brother Laszlo, who they have been keeping in Rikers. If Yogorov signs a statement against Alonzo then Carter will have Laszlo transferred to a safe facility. He gives in and Carter tells him that she's vetted judges to find one that isn't in Alonzo's pay, so that she can get a warrant issued for Alonzo's arrest. As she leaves, Yogorov tells her to select carefully because if she picks the wrong judge then they're both dead.
Later, Carter meets with Fusco outside his apartment and tells him what she's been doing. He wonders why she didn't turn to him for help and wonder if she doesn't trust him, and Carter insists that she's been protecting him. She gives Fusco the key to a safety deposit box and tells him that it holds everything she has on HR. Fusco refuses to take it Carter tell him that he's the best partner she's ever had, and the only one she can trust. Touched, Fusco insists that she's not going to take on Alonzo alone. Carter seemingly agrees and tells him to get his Kevlar vest and shotgun. As soon as he goes inside to get them, she throws away his car keys and drives off in her car.
Mitchell and the other crooked cops take the Russians down to the docks and prepare to execute them. Reese and Sam follow them there and prepare to open fire, figuring Carter hasn't allowed for the collateral damage. However, the FBI pull up before Mitchell and his men can shoot. FBI Agent Barnes confronts Mitchell, who claims that they're busting up a drug deal. Barnes has received tip and opens up Mitchell's car trunk, revealing the stolen heroin from the hijacking. As the FBI take both sides away, Reese figures that they're work is done and checks in with Fusco. Fusco tells him that Carter has escaped and figures that HR will kill her as soon as they realizes that she set them all up. Reese and Sam split up to track Carter down before it's too late.
Carter calls Judge Andrew Monahan and asks him to let her swear out an arrest warrant on HR. Monahan agrees to help her... but once he hangs up, he calls Alonzo.
Detective Carter is outside the precinct house when Paul approaches her and shows her his VA medical card. He says that he's gone into counseling and is doing better, and that he's working on a future for himself and his family. Paul gives Carter his number in case she or Taylor ever need anything from him.
Carter pulls over on her way to Monahan's home and calls Paul. He's keeping Taylor safe at his apartment, and Carter thanks him for taking care of her son. Taylor then takes the phone and they make small talk, and Carter apologizes for keeping him in the dark for the last eight months. Taylor says that there's a lot of people that care for her and she doesn't have to do everything alone. Carter simply says that she loves him and says that she'll call him the next day.
When Carter arrives at Monahan's, the judge ushers her into his study. Alonzo, Simmons, and their HR men are there with guns, and have spread a plastic sheet on the floor. Simmons destroys her phone and Alonzo admits that he killed his own godson to protect himself and HR. He says that he should have killed Carter with Cal, and Simmons prepares to shoot her. Carter tells them that she thought she could take down HR on her own, but she realized that she would need friends of her own to go up against Alonzo and his people. She then points out that it's possible to listen on a cellphone even if it's turned off. Finch plays back Alonzo's admission that he killed Cal as Reese bursts in shooting, taking out the other HR men. Carter grabs Alonzo and escapes outside with Reese, while Simmons calls in his people.
Outside, Reese wonders where they're going and Carter says that they'll turn Alonzo over to the Feds. A HR cop pulls into the driveway and Reese opens fire on him. By the time the officer can return fire, Reese and Carter have escaped with Alonzo. Simmons comes out and checks the car's mounted camera, and gets a clear image of Reese. He then puts a contract on Reese's head to every crooked cop and gang on the streets.