Emma drives Joey to a garage facility and tells him that they're going to meet a friend of hers and then she'll take Joey to Claire. When he wonders where Paul and Jacob are, Emma admits that she doesn't know when they'll arrive. She finally snaps at the boy when he keeps asking questions, but then assures him that everything will be okay.
The owner, Bo, steps out of the shadows and tells Emma that it's about time that he got there. Joey asks to use the bathroom and Bo directs him down the hallway. As Joey reaches the door, he hears a woman whimpering from behind another nearby door. He slips inside and sees a girl locked up inside of a cage. The woman, Dana, begs Joey not to leave her. However, the frightened boy runs off.
Olivia brings Carroll before the prison board, including Warden Gene Montero, and shows them footage of Ran breaking three of Carroll's fingers. Carroll then addresses the board, saying that he wants them to know exactly what Ryan is and what he does to prisoners.
At Claire's home, Debra has Claire tell her what Charlie said during the time that he held her prisoner. Claire explains that Charlie appeared to be some kind of soldier and acted on a code of honor. Ryan brings Claire tea as she says that Charlie was waiting for orders from Roderick, and Ryan remembers that Emma also received a call from Roderick. Claire wonders how many people Carroll has recruited and Ryan admits that they don't know. When Debra asks her not to engage any more of Carroll's people, Claire refuses, pointing out that the FBI hasn't done any better finding her son. All Debra can do is ask her is to tell them if anyone makes contact with her again. As Debra leaves, Claire begs Ryan to find Charlie, the man who can lead them to her son.
Emma tries to talk to Bo about Charlie but he ignores her. When Joey comes back, he tells Emma about Dana and insists that they have to help her. Bo hears them talking and angrily tells them that Dana is none of their business. Once he goes back to work, Emma tells Joey to stay there and goes over to talk to Bo, but he insists that they should just wait for Charlie's arrival.
Debra meets with Montero, who insists that he's approving Carroll's transfer because of the liability risk. As he leaves, he runs into Ryan and tells Debra to keep the man under control. Debra tells Ryan that the U.S. Marshals are transferring Carroll to another facility. Mike comes in, delaying them long enough for Ryan gets there to talk to Carroll privately. He asks why Carroll wants the transfer and wonders if he's going to meet with Roderick. Carroll feigns ignorance and says that he doesn't know a Roderick, and asks if Claire has rejected Ryan yet. Ryan figures that Carroll is changing the subject but the killer ignores him and the Marshals return to escort him out. Ryan goes back to Debra and says that he should go with the transfer team. Debra informs him that she's the only one with permission. Once she leaves, Ryan goes to the command center and has Mike run a check on Montero.
Emma asks Bo how he knows Roderick and the man says that he does favors for Roderick from time but he's not one of Carroll's followers. As they talk, Bo notices that Joey is gone and starts looking for the boy. Meanwhile, Joey grabs the keys from a shelf and goes back to Dana. He frees the woman and she runs to the outside door, telling Joey to come with him. He hangs behind and she leaves, and Bo runs in and demands to know what Joey has done. The boy runs out into the garage and hides beneath a truck, but Bo soon finds him and drags him out. Emma draws on Bo, telling him to let Joey go, and Bo manages to disarm her. As he prepares to shoot her, Charlie arrives with a captive Dana and tells Bo to let Emma go.
The Marshals take Carroll to the sally port van and Montero monitors the men. Ryan watches Montero suspiciously and then receives a call from Debra, who tells him that the chopper is inbound and everything is going as planned. She gets into one of the two escort vehicles and they take off with the transfer van, while a chopper flies cover overhead. Ryan checks with Mike, who has confirmed that Montero has a daughter... Dana. She's attending college and disappeared several days ago. Ryan confronts Montero, figuring that Carroll is using his daughter as a hostage. Montero denies everything, warns Ryan not to push him, and walks away. Ryan tells Mike to put Montero under surveillance.
At the garage, Charlie tells Emma that they're waiting for word that it's safe to move Joey. When she asks about Bo, Charlie explains that some people were attracted to Carroll's website that are useful, but that aren't part of the main group. They're letting Bo hold onto Dana for leverage and that once Carroll is free, they'll meet up with some of Charlie's ex-military buddies. Charlie asks about Paul and Jacob and, when Emma doesn't respond, assumes that they're dead. He assures Emma that they all do what they have to for Carroll and walks away.
Ryan has Mitchell review the video files they found on Charlie's computers at his warehouse. She discovers footage of the sally port and realizes that it's the same footage they saw of the actual transfer... and there's an edit. Ryan figures that Montero substituted the footage and confirms that Montero is leaving the building. The ex-agent calls Debra and tells her what they've learned, and Debra has the Marshals pull over. When the driver refuses to open the rear door, Debra draws a gun on him and orders him to do it.
Ryan and Mike drive to the gate and cut off Montero as he leaves in his car. They order him to open the trunk even though the warden warns them that they'll get his daughter killed.
The Marshal opens the back of the van and Debra and the others discover that Carroll isn't there.
Montero reluctantly opens the trunk, revealing that it's empty. Ryan demands to know what Montero has done with Carroll.
Olivia drives to a deserted warehouse, parks outside, and lets Carroll out of the trunk of her car.
Ryan assures Montero that Carroll's people will keep Dana alive as a hostage to his good behavior, and the warden finally tells the agents that Olivier told him to give Carroll to her. After they put Montero into custody, Ryan and Mike call Mitchell and have her track Olivia's GPS. She gives them the location of the lawyer in nearby Richmond and they drive off to intercept her and Carroll.
Carroll tells Olivia to keep driving for a few more minutes.
Charlie loads up supplies and Joey comes over to talk to him. The follower points out that Joey isn't supposed to be out, and promises that they're taking him to see Claire and that he just talked to her. Charlie admits that he screwed up and let the bad guys get Claire, and tells Joey that it will take longer than they anticipated to reunite him with his mother. Joey, skeptical, asks what's really going on and asks what will happen to Dana. Eager to comfort the boy, Charlie promises that she won't be harmed.
Carroll tells Olivia to park at the curb near a restaurant. He tells her that someone probably followed them and orders her to call Ryan. When she does, Carroll tells her to say, "Joe Carroll is killing me and because of you, Ryan." When she refuses, Carroll chokes her, forcing Ryan to listen over the phone as he kills the lawyer. Ryan offers to let Carroll kill him instead but the killer finishes off his defense attorney. Carroll then dons a suit that Olivia brought him and then goes into the restaurant. He spots one of his followers, David, on the mezzanine above him and nods in greeting.
When Ryan and Mike find Olivia's car, they confirm that the attorney is dead. A street worker tells them that Carroll went into the restaurant and they split up to search inside. Ryan spots Carroll and David and gives choice. Meanwhile, David takes his superior down a utility hall to an elevator to the parking garage. A security guard, Douglas, notices them but before he can move to investigate, a woman brushes against him in passing. She cuts open his stomach with a straight razor and then introduces herself to Carroll as Louise. The three of them then go to the elevator.
Ryan comes running up and finds the dead man. When he sees that the elevator is going up, Ryan goes to the stairway only to discover that David is waiting for him. David disarms him, takes his gun, and runs up the stairs. Ryan goes after him but David is waiting and gets the drop on him. Despite that, Ryan manages to take David down, but Carroll arrives and holds his nemesis at gunpoint. Carroll debates whether he should kill Ryan or not, and explains that he's spend nine years planning his great real-life novel. He finally decides not to kill Ryan and gives his gun to David. Louise says that it's time to go and they go to the roof of the parking garage.
As time runs out, Ryan reminds David that Carroll doesn't want him dead. He gets close enough to disarm David and then shoot him in the leg. He runs to the top of the structure only to watch as Louise and Carroll depart in a helicopter.
Charlie gets a call and tells Emma that they'll be leaving. When she asks what will happen to Bo and Dana, Charlie tells her to give him a few minutes. He then calls Bo out of the room to talk.
Once Debra and her men secure the parking garage, she tells Ryan that they lost the helicopter when it kept below radar. She insists that they'll find Carroll and his people and break them, but Ryan says that they have to start doing things differently. He looks at David and Debra, realizing what Ryan means, calls her men over for a briefing. Ryan tells the EMTs to give him a few minutes with the prisoners and puts on a pair of rubber gloves. He asks David how the pain is and David says he can handle it, and Ryan digs his fingers into David's leg wound.
Once he has the information he needs, Ryan and Debra take a FBI team to the garage. Bo's corpse is lying to one side, a bullet in the head. They find Dana locked in her cage and free her. She tells them that her captors took Joey with them.
The FBI team has Claire pack to go with them into protective custody. Ryan checks with her and admits that he doesn't know where they are taking her for reasons of security. When he tells Claire that Carroll won't win, she insists that it's not a game and that Joey's life is at risk. Disgusted, she walks out past Ryan.
Carroll and Louise drive to a large manor in the country and a group of people emerge to greet them. Emma is there and runs to embrace her mentor. Joey comes out and Emma motions him over to see his father. When Joey doesn't move, Carroll goes over and the boy says that he recognizes him. Carroll, on the verge of crying, says that he's Joey's father.