The Machine monitors Reese and Carter as they leave Judge Monahan's house and head for the Federal Building with Alonzo Quinn.
Monahan asks to see Simmons and wonders what they're going to do now that Carter has Alonzo. Simmons assures him that no one will be charged and tells the judge that they have checkpoints on the all the roads so that she'll never get to the Federal Building. As for the evidence, no one will kill Carter until they have the evidence that she has on HR. Simmons says that they need to come up with a story and asks if Monahan has a gun. Once the judge points it out, Simmons gets it, says that they'll make it look like a robbery and murder, and then kills Monahan. Officer Brady comes in and Simmons tells him that Monahan would have talked. Simmons tells him to get rid of the gun and bring Carter and Alonzo to him without harming Alonzo. As for Reese, Simmons tells Brady to have their people shoot on sight.
Finch is out walking Bear when a nearby payphone rings. He takes down the new Number that The Machine passes on.
Reese and Carter get Alonzo onto a subway train and Carter checks his wound. He warns them that they're out numbered in his city, and Reese tells Carter that Finch is sending the cavalry.
Fusco is at home checking on his son Lee, who notices that he's wearing a key around his neck. The detective explains that he's keeping some evidence for a friend and tells him to sleep. Fusco finds Sam checking the milk in his refrigerator and tells him that Reese and Carter need help getting Alonzo into Federal custody.
On the subway train, Carter apologizes to Reese for getting him into the situation. She says that she'll take Alonzo in on her own, and he wonders what it is that makes her want to do everything on her own. Finch interrupts to warn Reese that he's received several Numbers. They're all prior aliases for one person: Reese. HR has put a bounty on his head and distributing Reese's photo. Elias has called to say his people will be sitting it out, but they're the only ones. The Trinitario gang comes in as Finch warns Reese that every criminal in New York is trying to kill him. They advance on Reese and prepare to attack him.
When the subway train comes to a stop, Reese kicks the defeated gang members out. As they switch trains, an announcement has made that all train service is suspended to Manhattan. When Alonzo threatens to stay where he is, Carter promises to stop him. Reese tries to call Finch but Alonzo reveals that he stole the cellphone. He smashes it on the floor and warns that his men will have every route blocked. Carter drags him off, figuring that they need better camouflage.
Finch realizes that he's lost contact with Reese, and informs Sam of the situation. She suggests that he ask The Machine for Reese's location. When Finch points out that it doesn't speak to him, Sam suggests that he talk to Root. Finch brings up the Federal Building on the map and tells Fusco and Sam to split up and cover the two routes to the building. He then goes to see Root in her cage. Bear goes with him but then runs off. Finch unlocks the cage and brings her a tray of food, and then says that she must have rewritten the DNA of The Machine's code so she can speak with it. Root tells him that he has the relationship with The Machine that he wants, and The Machine respects that. Her relationship is more intimate. Root realizes that it's about Reese and offers to talk to The Machine if Finch sets her free. Finch wonders how he could let her go when he knows that bad things will happen, and Root tells him that bad things will happen regardless. She wonders how many helpers Finch went through before he found Reese, and Finch locks her back up and walks away.
Reese and Carter hijack an ambulance. While Reese rides shotgun with the driver, Carter tends to Alonzo's wound.
Simmons meets one of his HR men, Petersen, at the Brooklyn Bridge checkpoint and explains what happened. He figures that Reese is hiding in plain sight.
Sam checks the subways while Fusco mans the Brooklyn Bridge. Neither one of them find any sign of Reese or Carter.
The ambulance arrives at the Brooklyn Bridge. Reese tells the driver to go on through and hunches his head down low. Simmons notices a bloody handprint on the back of the ambulance and orders his men to stop it. Reese steps down on the accelerator and runs the barricades, and Fusco provides cover fire. He tells Sam that they got through... just as Simmons finds him and knocks him out, and then crushes his phone.
At the subway station, Sam updates Finch on Reese's status and warns that Fusco may be dead. She asks him if he wants her to go after Reese and Carter, or Fusco. Finch glances at Root on the monitor and then tells her to locate Fusco.
Simmons, Petersen, and Officer Miller take Fusco to a fortune cookie manufacturing factory wake him up, and assure him that no one will hear him scream. Petersen holds up the keychain with the safety deposit key and Simmons asks Fusco when he last saw Carter. When Fusco refuses to talk, they start beating him. Simmons asks what the key opens and figures that it's a safe deposit box. When Fusco still refuses to talk, Simmons breaks one of his fingers and says that if he doesn't tell them then he'll break the detective apart limb by limb.
Reese and Carter abandon the ambulance four blocks from the Federal Building and take the driver's cellphone, but spot more HR officers. Another gang, the Bloods, spots them and the trio duck into a building. Reese calls Finch and tells him that they're in the city morgue. Finch explains that HR has Fusco and Sam is looking for him, and Reese assures Carter that Sam will find him.
Sam gets into a car with a HR man and quickly handcuffs him to the wheel. She then puts a handcuff in his hand and pulls the pin, and tells him to call Simmons and find out where they're keeping Fusco. The beat cop warns her that Simmons will kill his entire family if he crosses his boss. After a moment, Sam tosses the key in the back and leaves.
Carter tries to work out how to get to the Federal Building. Reese suggests that they wait until sunrise in the hopes that HR will be reluctant to shoot. When Alonzo warns them that they can't escape his people, Reese injects him with a sedative and they stuff him in a morgue drawer.
Simmons continues torturing Fusco, who refuses to break. The HR man warns that they'll go after Lee and Fusco finally tells them the address in Hoboken. He warns that it won't be open but Simmons figures that he can get in. Simmons has Miller go to get Lee while Petersen watches Fusco. Brady calls to tell Simmons that the Bloods spotted Reese going into the morgue. Simmons tells Brady to bring everyone there so they can finish it.
As Carter puts Alonzo in a drawer, Reese loads up with autopsy tools. He points out a scar that a Hezbollah surgeon left him on his chest, and Carter shows Reese a scar from a landmine detonation. She then shows him her worst scar she has: the C-section when she almost lost Taylor. Carter asks what his closest injury was, and Reese holds up a bullet and says that there was a time when he was going to say goodbye, but he lost them instead... and lost himself. When she asks what stopped him from killing himself, Reese says that he got into a fight in the subway and a cop brought him to her. Reese kisses her and says that she changed him.
Finch calls to tell Reese that the police are checking on the morgue, and tells them to leave. Reese checks and discovers that they're already surrounded, and they both prepare to fight.
Brady takes his people into the building and tells the guard, Ed, that they have reports of vandals. When he objects, they handcuff him and pull the lights.
Finch brings Root breakfast at four in the morning and says that he may not be back. Root says that it's not too late for her to save Reese, but Finch refuses. She says that she hopes that he'll trust her some day and offers her condolences at his lost.
Simmons goes to the bank in Hoboken and calls to tell Petersen that Fusco lied. The HR man figures that they'll track down the right bank eventually. Fusco speaks up, saying that he'll talk, but Simmons tells Petersen to eliminate him and Lee.
HR goes through the building, tossing rooms, and Reese tells Carter to check the supply room for chemicals. When she comes back, she discovers that Reese has left through the air vent. Carter calls to him through the door, telling him not to throw away his life. Reese tells her to make a run for it while he draws them off, and tells her to make sure Alonzo gets what he deserves.
Petersen calls Miller at Fusco's apartment, who confirms that he has Lee. Miller draws a gun on Lee, and Fusco begs them to let Lee go. Petersen tells his man to put Lee on the phone and let Fusco listen as his son dies. Fusco tells Lee that he's there with him and everything will be okay, and tells his son to close his eyes. A gunshot echoes out and Fusco breaks into tears. Sam then comes on the phone and tells him that it will be okay and Miller is dead. Fusco thanks her and she warns that she can't be there for him because she had to choose. He tells her that she did good and Sam apologizes as Petersen hangs up.
The HR cop takes out his gun and prepares to kill Fusco. Fusco tells him that guys like the two of them can only hope that someone holds their hand as they bleed out. When Petersen points out that they broke his finger, Fusco says that's why it was no big deal to break his thumb. He slips his handcuffs and grabs Petersen, choking him to death with the handcuffs.
Finch goes to the morgue and tasers the HR man standing watch. He then goes to work on the power.
Reese opens fire on Brady and the others. He takes out one man but Brady manages to wing Reese, who runs out into the street. As Brady runs out after him, Finch gets the lights and the alarms on in the morgue. Reese ducks into an alley and tells Finch to get Carter to safety. Finch gets on the loudspeaker and tells Carter that she can leave the building. Carter wakes Alonzo up and drags him out.
As Reese goes down the street, two officers come over and arrest him. Finch tells Reese that he reached two of the NYPD's honest cops and told them that Reese was brandishing a weapon. The officers take him into custody.
As the sun rises, Carter takes Alonzo up to the Federal building. He warns her that she'll never conviction because it's his city, but Carter tells him that it's not his city anymore. Carter hands Alonzo over to the Feds.
The police bring in the remaining HR cops except for Simmons, while Alonzo is booked on suspicion of being the head of HR.
Finch goes to see Carter at the station and congratulates her now that she's been promoted back to detective. He informs Carter that Reese is being held at another station and his lawyers are working to get him released. Carter asks him about his computer and explains that she worked out that Finch had some kind of super-computer. Her phone rings and she tells Finch that she'll check on Reese later. As Finch walks off, Carter takes the call from Fusco. He's watching Lee going in for hockey practice, and tells Carter that it's good to have her back. As Fusco hangs up, Sam gets in the car with him and points out that Fusco looks like crap. He turns around and thanks her, truly, for what she did. Sam tells him to shut up and drive.
That night, Carter checks in on Reese and echoes their first conversation. As she leads him out, Carter admits that she hasn't been able to locate Simmons. Reese assures her that they'll find him, just as Finch pulls up. He tells her that if his Number was up, he was glad he was with her. The payphone near Finch rings as Simmons steps out of the alleyway and shoots Reese in the side. Carter goes for her gun and she shoots Simmons just as Simmons shoots her in the chest. Simmons staggers off while Reese crawls to Carter and tells her that he's there. She says that she needs to see Taylor, and asks Reese to promise to look in on him. Reese tells her that Taylor knows as Carter dies in his arms.