Neal sits on the rooftop patio at home, drawing on a New York City map while referring to a photo of the music box. June brings up a visitor, Alex Hunter. Neal offers to steal the music box, and give it to Alex when he's finished with it. She says she'll be back at 6:00 the next evening. If he's free of his tracking anklet, she'll give him what he needs.
At the office Neal apologizes for being late. Burke unobtrusively plucks a long brown hair off Neal's shoulder. Agent Kimberly Rice, a rising star in the Bureau's kidnapping and missing persons division, wants to borrow Neal for a case in which he has ties to the prime suspect. Lindsay Gless was taken in a home invasion the night before. Her father is corporate CEO Stuart Gless, whose company bonds Neal was convicted of forging. The suspect is Ryan Wilkes, who runs his own crime syndicate. Wilkes and Neal tried teaming up once, unsuccessfully.
Word on the street is that Wilkes is in New York, and Rice's agents found traces of plasticine clay in a lock at the Gless house. Copying keys is Wilkes' MO. Neal says that Wilkes used to have lunch every Thursday at a particular restaurant which has only one valet. Hughes agrees to let Rice borrow Neal. In response to Rice's question, Neal says the last time he saw Wilkes was when the latter tried to kill him.
The restaurant's security video produces a positive identification of Wilkes. Rice and Neal arrive at the Gless house, where Stuart Gless receives Neal kindly since the latter is there to help get Lindsay back. Neal's direct questioning of Lindsay's father doesn't sit well with Rice, who informs Neal that he's just "a tool in her belt". She then sends him to wait in the car.
Meanwhile, Burke can't shake the feeling that something's wrong about the Gless case. He goes to the scene and finds Neal in the car. They check a nearby alley and find a coat check stub, presumably dropped by Wilkes' lookout. Neal recognizes it as being from an underground club that's one of Wilkes' old hangouts. Rice is not pleased to see Burke at her crime scene.
Mozzie expresses his disapproval of Neal's being the bait to catch Wilkes, whom Neal had ripped off. Neal says he's going along because he'll have to lose his tracking anklet for the operation. Alex won't talk to him while he's wearing it. At the office Burke sees the signal when Neal removes his anklet. Jones explains that Rice approved removing it.
Neal enters the club's courtyard and disappears from sight. At the office Burke has coffee with Stuart Gless, who came there to wait because being at home was too stressful. Gless says he's worried about "the meeting". The kidnapper had called him and asked for a meeting with Neal in exchange for Lindsay. It seems too easy. Burke phones Neal and tells him to get out now; he's the ransom. Before Neal can act, someone tasers him unconscious.
The next morning Rice and her agents enter the office, as one of them reports that a silver van with no license plate was seen leaving the club. Burke angrily accuses Rice of knowing all along about the club and what would happen. Confronted by Hughes, Rice is forced to admit she agreed to the face-to-face meeting with Neal in hopes of following the kidnapper back to Lindsay. She had agents all over the street, but Neal was taken in their one operational blind spot. Hughes puts Burke in charge, with Rice reporting to him.
Neal awakens in the back of the van, reunited with Ryan Wilkes. As the van comes to a stop, Wilkes warns him not to try to run or yell for help. They're at a travel agency, which Wilkes explains booked travel to New York for a Thomas Loze. Wilkes wants Neal to get Loze's itinerary from the receptionist. If he isn't back with it within two minutes, a sniper on a nearby roof will kill the receptionist. Neal immediately understands: Wilkes wanted a "front man" to avoid being the face on the agency's security camera.
Neal enters the agency and pretends to be an overworked, underappreciated assistant at a concierge service. He tells the receptionist that he has several five-star dinner reservations to arrange for Thomas Loze, but he lost Loze's itinerary. After some persuasion, she gives him the itinerary. Neal sees an advertising poster and adds that he knows someone who might be interested in the agency's rewards program.
Mozzie receives an e-mail from the travel agency addressed to "Dante Haversham", and excuses himself from a Parcheesi game with June. Neal delivers Loze's itinerary, then tauntingly says he's starting to wonder if Wilkes really has Lindsay. They get back into the van and take off. At the office the team watches a DVD which Stuart Gless received. It's a proof-of-life video of Lindsay, standing in front of a cracked brick wall with some "funky" windows. In the background of the audio is the sound of a tugboat horn. She's being held somewhere on the waterfront.
As Neal hoped, Wilkes takes him to Lindsay. Neal assures her that the FBI is looking for them, and notes that the guard is eating Chinese takeout. Elizabeth phones her husband and tells him an agitated Mozzie is at their house. Having seen Lindsay, Neal agrees to "round two" of Wilkes' scheme. Burke comes home, and Mozzie explains that the e-mail to Dante Haversham is a distress signal from Neal.
Wilkes has arranged to have Loze's limousine intercepted so that Neal can take over as the driver. Neal is to steal a titanium briefcase Loze will be carrying, and deliver it to Wilkes at 4:00. Then their business will be concluded. Burke's team tracks Neal's visit to the travel agency. Thomas Loze is actually Edward Reilly, the go-to guy when VIP criminals want something valuable moved. He hand-delivers everything himself, and is extremely dangerous. Wilkes is using Neal to rip off Reilly, who arrives in New York in an hour.
Burke and Rice greet Neal at the airport and bring him up to date. Reilly would hunt anyone who double-crossed him to the ends of the earth; no wonder Wilkes wanted someone to hide behind. Neal remembers the name of the restaurant the guard's Chinese takeout came from. Before leaving, Burke gives Neal a two-way transmitter so that Jones and his team can track him.
Neal is then greeted by Mozzie, who proposes getting Reilly to give them the briefcase freely instead of Neal trying to steal it. Equipped with fake credentials, they pose as federal agents and order Reilly to open the case. Inside a hidden compartment are dozens of pure gold cards. They pretend they're about to call in their find when Reilly falls for their scheme and gives up the briefcase, rather than be caught with it.
Burke's team arrives at the dock nearest the Chinese restaurant, but there are several buildings in the area. It's almost 4:00, and Neal is at the delivery point. Neal gives Wilkes an apparently empty briefcase, and stalls while the team locates the building where Lindsay's being held. Wilkes calls the guard and orders him to kill her, leaving the phone on speaker while he does so. At that moment Burke's team breaks down the door and rescues Lindsey.
An infuriated Wilkes hurls the case against a nearby building in frustration, breaking open the hidden compartment and revealing the gold cards. Wilkes is about to kill Neal when Jones' team gets the drop on him. Neal arrives at the dock just in time to see the joyous reunion between father and daughter. Neal tries again to apologize, but a grateful Stuart Gless shakes his hand and says they're even now. Jones arrives moments later with the tracking anklet, but Neal's gone.
Alex is waiting when an anklet-free Neal returns home. She hands him a paper flower, which he unfolds and reads. He chuckles and says, "You go halfway around the world chasing something, and the whole time it's in your own backyard." Alex says she'll see him soon, and leaves. Neal then goes to the office, where Burke confronts him about Alex and the music box. Burke warns that if Neal tries to steal the music box, he will catch him. "You know, you can either go back to wearing an orange jumpsuit and pining for the girl who got away…or you can stay here and do something good with your life. Your choice."