As Reese and Carter leave Judge Monahan's house with Alonzo Quinn, The Machine monitors them from a surveillance camera.
Monahan demands to see Simmons and Officer Brady with HR brings his superior in. The judge wonders what they're going to do now that Carter has Alonzo, and Simmons says that they'll make the break-in look like a robbery. He asks Monahan if he has a gun and, once the judge provides it, shoots him dead with it. Simmons tells Brady that Monahan would have cracked and given state's evidence, and tells him to get rid of the gun and then bring Carter and Alonzo to him. He tells Brady to make sure that Alonzo is unharmed, and to put out a shoot-to-kill order on the Man in the Suit.
As Finch walks Bear, The Machine calls him from a nearby phone booth and gives him a new Number.
Reese and Carter take Alonzo to a subway train going into New York. As Carter checks his wound, Alonzo warns them that it's his city and they're outnumbered. Reese calls Finch and then tells Carter that the hacker is bringing in reinforcements.
Fusco checks on his son, who is going to bed, and Lee notices that his father is wearing a key on a chain around his neck. The detective says that he's keeping some evidence for a friend and tells Lee to go to sleep. When Fusco goes to the kitchen, he finds Sam going through his refrigerator. She tells him that Reese and Carter need help getting Alonzo to the Federal Building.
On the train, Carter apologizes to Reese for getting him involved and offers to take Alonzo the rest of the way on her own. Reese wonders why she wants to everything on her own and Carter asks him why he wants to save everyone but himself. Finch calls to tell Reese that The Machine has given him several new Numbers. They're all aliases for one man: Reese. HR has put out a contract on Reese and providing everyone with the photo from Brady's police car. Elias has assured Finch that his people won't join in the hunt, but Finch warns Reese that they're the only ones. Members of the Trinitario gang enter the train car as Finch tells Reese that every criminal in New York is now after him. The Trinitario's leader comes up to Reese, who just smiles.
When the train pulls into the next station, Reese kicks the unconscious gang members out of the car and prepares to switch trains. However, the stationmaster announces that all trains going into Manhattan have been suspended by order of the police. Reese tries to call Finch but Alonzo reveals that he's stolen Reese's phone. The deputy mayor smashes it on the floor before Carter can stop him, and warns that his organization will block every route to the Federal Building. Carter tells Reese that they need better camouflage.
When Finch realizes that he's lost contact, he calls Sam and tells her the situation. She points out that he could ask The Machine, but Finch notes that it doesn't speak to him. Sam suggests that he talk to Root, and Finch tells Fusco and Sam to separate and cover the two main routes to the Federal Building. He then goes to the library cage where he's keeping Root. He insists that she must have rewritten the DNA of The Machine's coding so she could speak to it, but Root corrects him. She says that Finch has the relationship with The Machine that he wants, and the Machine respects that. However, Root says that her relationship is more intimate. She realizes that Reese is in trouble and offers to get The Machine's help... if Finch will release her. Finch says that he can't do that when he knows that bad things will happen as a result, and Root points out that bad things will happen anyway. She asks Finch how many helpers he's had before Reese and how many died, and Finch leaves without a word.
Reese and Carter hijack an ambulance and Reese rides shotgun while Carter bandages Alonzo's wound.
Simmons is at the Brooklyn Bridge checkpoint when one of his HR operatives, Detective Petersen, shows up. His superior notes that Reese isn't very subtle and figures that he'll hide in plain sight.
Fusco checks the Brooklyn Bridge and spots Simmons and Petersen, while Sam checks the subway station. The ambulance arrives at the bridge checkpoint and Reese tells the driver to go through. The police wave them through, but Simmons notices a bloody handprint on the ambulance door and realizes that it's Reese. His men open fire and Reese jams down the accelerator pedal. The ambulance goes through the barricades and, thanks to Fusco providing cover fire, successfully escapes. As Fusco checks in with Sam, Simmons knocks him out and smashes his cellphone.
At the subway station, Sam warns Finch that Fusco may be dead. She asks him if he wants her to go help the detective, or assist Reese and Carter. Finch tells her that Fusco is defenseless and to find him, and that Reese and Carter are on their own.
Simmons has Petersen and Officer Miller drag Fusco to a fortune cookie plant and wake him up. Petersen hold up the key chain from around Fusco's neck and Simmons asks Fusco when he last saw Carter. Fusco refuses to talk and Miller and Petersen beat him. They break one of his fingers but Fusco remains silent, and Simmons tells him that they'll tear him apart limb by limb if they have to.
Reese and Carter get within four blocks of the Federal Building and abandon the ambulance. They tie up the driver and take his cellphone, and head for the building. However, they discover that another gang, the Bloods, are heading toward them. Reese breaks the lock on a door and goes inside with Carter and Alonzo. The gang passes them by and Reese reestablishes contact with Finch. He confirms that they're in the city morgue, and Finch tells him that HR has Fusco. Carter realizes that her friend is in danger and Reese assures her that Sam will find Fusco.
Sam gets into the patrol car of a HR beat cop, takes his Hot Pocket, and replaces it with a hand grenade. She cuffs him to the wheel and then pulls the pin, and tells him to call Simmons and get Fusco's location. The beat cop refuses, insisting that Simmons will kill his family and Sam can't do anything worse to him. After a moment, Sam tosses the grenade pin in the back seat and walks away.
At the morgue, Reese tells Carter that their best bet is to wait until sunrise so to reduce the chance that HR will shoot them out in the open. Alonzo, listening, tells them that it won't do any good and Reese injects him with a sedative to keep him quiet. They then stuff the deputy mayor in a morgue drawer for the time being.
When Fusco refuses to tell them the safe deposit box location, Simmons threatens to go after his son. Fusco gives them the address of a bank in Hoboken, and Simmons figures that he can get a warrant and get inside despite the hour. He then tells Miller to get Lee as insurance and orders Petersen to watch Fusco. Meanwhile, Brady has contacted the Bloods, who doubled back and found the broken lock on the morgue door. Brady figures that Reese and Carter have gone to ground and Simmons tells him to bring their men in to finish it once and for all.
Reese improvises weapons out of the tools in the morgue and shows Carter the scar on his chest that a Hezbollah surgeon left there. Carter shows him a scar from a landmine detonation, but says that the worst scar she ever got was the C-section from when she almost lost her son Taylor. She asks Reese what his closest near-death experience was, and he takes out a bullet. Reese explains that there was a time when he was going to say goodbye to his old life, but he lost himself. Realizing that Reese kept the bullet for himself, Carter asked him what changed his mind and Reese says that she found him. Kissing her gently, Reese tells her that she changed him. Finch calls and tells them to leave because the police have arrived. Reese confirms that the HR cops have already surrounded the morgue, and he and Carter prepare to fight.
Brady and his men enter the building and tell the guard, Ed, that they received a report about vandals. When he says that he hasn't seen anything, Brady handcuffs him and shuts down the power to the building.
Finch brings Root an early breakfast and warns that he may be gone for some time... or may never come back. She tells him that it's still not too late to save Reese if Finch releases her, but he still refuses. Sighing, Root says that she hopes that Finch will trust her some day and offers her condolences on his loss.
Simmons arrives at the Hoboken bank and confirms that Carter's safe deposit box isn't there. He calls Petersen and tells him to kill Fusco and Lee. Fusco offers to talk, but Simmons figures that they'll find the right bank eventually.
HR works its way systematically through the morgue. Reese tells Carter to check the supply closet for any chemicals they can use. However, when she comes back she discovers that Reese has used the air vent to bypass the barricaded door and go out in the hallway. Carter calls to him through the door, begging him not to throw away his life. Reese tells her that when he draws off the cops, she should make a run for the Federal Building with Alonzo. Before he leaves, Reese tells Carter to make sure that Alonzo gets what's coming to him.
Petersen calls Miller, who has Lee, and Miller prepares to shoot Lee. Fusco begs them to let his son go, but Petersen has Miller put Lee on the phone so that Fusco can hear him die. The detective tells his son that he's there with him, and tells him to close his eyes. A gunshot rings out over the phone and Fusco breaks into tears. However, Sam then gets on the phone and tells him that Lee is safe and she killed Miller. Fusco thanks her for choosing his son to save, and tells her that she did good. Sam apologizes as Petersen shuts off the cellphone. Petersen then prepares to shoot Fusco, who says that they're both alike and that the best they can hope for is someone holding their hand when they die. The crooked detective points out that they broke Fusco's fingers, and Fusco says that's why it was easy for him to break his thumb as well. He slips his hands out of the handcuffs and then uses them to strangle Peterson until the man dies, twitching to death on the floor.
Finch arrives at the morgue and claims that Simmons sent him. He gets close enough to the man on watch to taser him unconscious, and then works to restore the power.
Reese opens fire on the HR cops, taking all of them out but Brady. Brady manages to wing him and Reese is forced out onto the streets. As Brady goes after him, Finch gets the power working, setting off the alarms. Reese tells Finch to get Carter to safety, and Finch announces over the loudspeaker that Carter can leave the building. Smiling in satisfaction, Carter gets Alonzo out of the morgue drawer and drags him off.
As Reese runs down the street, two NYPD officers come over and arrest him for brandishing a firearm. Brady is forced to retreat while Finch tells Reese that he found two honest cops and filed the charge against Reese to get him arrested.
As day breaks, Carter arrives at the Federal Building. Alonzo warns her that she'll never get a conviction against him in his city, but Carter tells him that it's not his city anymore. She then hands Alonzo over to the Feds.
The police are soon arresting Brady and all of the other crooked cops. The Machine confirms that only one of them has escaped: Simmons.
Finch catches up to Carter as she receives a promotion back to detective. He tells her that Reese is being held at another station and that his lawyers should soon get him released. Carter casually mentions Finch's computer, and explains that she worked out that he's using some kind of super-computer to hack the government records and find potential victims. Finch doesn't correct her misunderstanding and leaves when Carter's phone rings. It's Fusco, who is watching Lee go to hockey practice. He tells Carter that it's good to have her back. As he hangs up, Sam gets into the car with him and Fusco thanks her, truly, for what she did. Sam, clearly uncomfortable, tells him to shut up and drive.
That night, Carter goes to get Reese out of jail. As she takes him out, Carter admits that she hasn't been able to track down Simmons. Reese figures that they'll find him eventually. Finch parks across the street and gets out of his car while Reese tells Carter that he's glad he was with her if his Number had to come up. The payphone near Finch starts ringing... and Simmons steps out of an alleyway and opens fire. He wounds Reese and then shoots Carter in the chest as she draws and shoots, winging Simmons. He runs off and Reese crawls to Carter, cradling her to his chest. He tells her that he's there and that she'll be okay, but Carter knows better. She says that she needs to see Taylor, and makes Reese promise to look in on her son. Reese tells her that Taylor knows that she loves him... and Carter dies in Reese's arms.