Peter brings the music box to Neal's apartment to show Mozzie. The cherub key opens another compartment inside the box's lid, revealing a second music comb. Neal snaps it into place, and the Mozart sonata plays while Mozzie records it. The box's code is geographical coordinates encoded in five musical tones. After Mozzie finishes recording, Peter takes back the box and nixes Neal's suggestion of using it to flush out Fowler. Tomorrow, they're back to business as usual.
Neal remembers that the box and the key were together when they stole it. Alex Hunter must have found the second comb while she had the box. Then why did she return it to Neal? And where is she now?
Peter returns the box to Diana's apartment and tells her that Neal seems to care now only about finding Fowler. Diana reports that Fowler checked the balance in an old bank account, but they couldn't locate him because he did it remotely. He didn't have much money when he disappeared. Peter recalls that suspicious circumstances in Mrs. Fowler's murder had delayed finalizing the insurance claim. If they put some cash in the account to make Fowler think the claim's finally come through, they can track him when he makes a withdrawal.
Neal tells Mozzie that pieces of a Spanish silver collection Alex fenced have been reappearing. They meet with their old contact Hale, who warns that if the thief keeps this up the NYPD will make the connection. To find Alex first by using FBI resources, Neal decides to con the Bureau.
At home Neal explains to Mozzie that for Peter, back to business as usual means pulling from the reserve of active case files. Neal is allowed to bring those files home to review. He wants to plant a fake case file for Peter to find. The conversation is briefly interrupted by June, who's leaving town for a few days. In accordance with their housing agreement, Neal will care for her pug Bugsy while she's away.
Neal and Mozzie create a fake file about the stolen Spanish silver, which Neal slips in with the other files. Peter finds it and takes the bait. The NYPD missed that each theft included at least one item from the same collection. Insurance policies gave the Bureau three other owners of the silver pieces. Peter says they'll stake out the one who called in a vacation watch to their home security company starting tomorrow.
A withdrawal is made from Fowler's account within an hour of the "insurance claim" deposit. A traffic camera caught Fowler in the area of the ATM, and Diana goes to check it out.
Listening to the Mozart sonata in Neal's apartment, Mozzie has come up with a string of letters but can't decode them. He knows an antique shop owner who's also a code maker, with a knack for hiding codes in gadgets. Neal leaves to join the stakeout, knowing that Alex always does rooftop reconnaissance from one block away. In the van before Neal arrives, Diana reports to Peter that Fowler had been staying in short-term housing under the name Aaron Burgis. He left two days ago. She checked the alias and got a big hit: a purchase of explosives. Peter is hesitant to tell Neal.
Neal finds Alex and points out the van. No one knows that Alex no longer has the music box, so she's still a target because of it. To make a living and keep a low profile, she's been stealing back items she previously fenced and fencing them again. Neal tells her that he used the FBI to find her before NYPD did. Alex tells him she didn't crack the music box's code. To get the target off her back for good, Neal asks her to steal the music box from Diana's apartment that night and donate it to the Russian museum. Diana's in the van, and her girlfriend works the night shift.
Peter tells Diana to look into all Fowler's activities as Aaron Burgis, but not from the office. Neal arrives at the van just as Diana's heading home, and is helpless in the face of this unexpected turn of events. After expressing his appreciation for Neal's trust the past few months, Peter tells Neal about Fowler's purchase of the explosives that blew up the plane.
Alex has just cracked the safe in Diana's apartment when Diana arrives. She grabs the box and escapes out the bedroom window. Diana hears her and calls "Christie?" as she goes into the bedroom. She runs to the open window and sees it's been jimmied, then discovers the empty safe. When Peter receives the news, he is furious with Neal.
The newspapers report that the music box was delivered anonymously to the Russian Heritage Museum. It will be displayed in an invitation-only showing before being sent home to St. Petersburg. Peter angrily takes Neal off the pursuit of Fowler.
Mozzie visits his antique dealer friend, Akhiro Tanaka. While Akhiro's in the back room making a copy of the code, Neal comes into the shop and brings Moz up to date. Akhiro returns and proposes dividing the code into two parts, with he and Mozzie each taking half. He invites Moz into the back. Neal starts to leave, then sees an antique revolver on the counter and takes it.
The museum won't budge on the invitation-only rule, so Peter and Diana stake out the place. Diana is also continuously monitoring Neal's anklet, which shows he's at home. As Bugsy watches, Neal suits up with the antique gun and a forged museum invitation. Now he breaks out the tracking anklet key he lifted from U.S. Marshal John Deckard during the Jack Franklin manhunt. He removes his anklet, then looks at Bugsy.
Fowler arrives at the museum and bribes the greeter to let him in. Peter follows and flashes his badge. Inside the museum Fowler sees Peter and hurries away, eventually locking himself inside an upstairs gallery that's closed for renovation.
Mozzie enters Neal's apartment, excitedly reporting a breakthrough in cracking the code. Then he realizes Neal's not there. The tracking anklet is around Bugsy's neck, and bullet casings are on the table. Moz keeps his earlier promise to tell Peter if Neal was going to do something stupid.
Neal gets into the museum before Diana can stop him. In the courtyard he looks up and sees Fowler through a second-floor window. He runs upstairs and out onto a small balcony. Long streaming banners hang from flagpoles outside each window, and Neal uses one to swing across the courtyard and smash through the window of the room where Fowler is.
Neal fires a shot at Fowler and growls, "That's the only warning you get. Tell me why you killed Kate!" Fowler denies trying to kill Neal and Kate on the plane. "Jesus, Caffrey, you think you're the only one that lost something? You think I wanted to spend the last year of my life chasing you and a stupid box? It cost me everything! My career is over. My wife is gone.''
Neal is about to pull the trigger when Peter finally breaks through the locked door. Peter implores Neal to put down his gun, because Neal isn't a killer. After a tense pause, a trembling Neal finally surrenders his gun. Diana handcuffs Neal and takes him away. Fowler says again that he didn't kill Kate, and Peter declares that Fowler will tell him who did.
In Peter's office, Fowler describes trying to put his life back together but wanting only vengeance for his wife's murder. One day an anonymous phone call pointed him directly to her killer. He found the person and took his revenge. A few days later he received a video in the mail, followed by another call. The caller offered to destroy the video if Fowler accepted a transfer to OPR and got him the music box. Fowler traced the box to Neal, who in fact didn't have it and was in prison anyway. So Fowler went after Kate, figuring she knew where Neal kept it. The mystery blackmailer has power and influence like Fowler's never seen before.
Fowler set up Neal and Kate's getaway as part of Operation Mentor. Kate had asked for the explosives, because she believed that just getting far away wouldn't keep her and Neal safe. She had planned for them to bail out over the water, then blow up the plane to make everyone think they were dead. However, Fowler wasn't the person she called just before the bomb exploded.
Diana comes in with Neal's tracking anklet, which the marshals have reset. Peter orders her to put it back on Neal, and to take him home.
Asked about his meeting, Fowler explains that he had been trying all along to get to his blackmailer. He finally got a meeting with the go-between, but didn't know in advance who it was. Fowler recognizes Patchwork Man as Julian Larssen, with whom he trained in Special Forces. However, he hasn't seen Larssen in years and had no idea Larssen was involved in this.
Diana reports that Akhiro has been found dead in his antique shop, shot twice. At the scene Peter and Diana hear the Mozart sonata, which a detective says was playing when NYPD arrived. On the table is a notebook containing musical notations and the word "Eureka." The shop's security video is paused on a shot of Neal during his earlier visit.
Meanwhile, Alex visits Neal at home. He offers her a drink while ignoring his buzzing cell phone. Alex is both glad that she's no longer a target, and sad that the search for the music box is suddenly over. She reaches into her purse just as Peter and Diana storm in with guns drawn. However, Alex is reaching for only a pen and notepad. She gives Neal her phone number and heads for the door.
After Alex leaves, Peter and Diana tell Neal that Akhiro's dead and they were afraid he was next. Neal tells them that he wasn't alone in the antique shop.
Mozzie sits on a park bench, enjoying a cup of tea. Julian Larssen walks by and quietly fires a shot into Mozzie's chest. As Mozzie puts his hands to the wound in stunned shock, Larssen casually sits down next to him and searches his pockets while pretending to be concerned. He takes a notebook from Mozzie's inside jacket pocket and wishes him a good day. As Larssen walks away, Mozzie topples over on the bench and loses consciousness.