Peter finds out what Fowler has been up to a laughing scheme - it’s a way to embezzle money. Neal dips out early saying he has to meet someone for lunch when really he is meeting with Alex. She tells him that the music is in the Italian Consulate.
Neal sets up a meeting with Fowler to get closer to the music box.
Peter realizes that Neal is up to something. He notices that he is pretty much staking out an area. He follows Neal to his meeting with Fowler.
The next day, Neal meets with Alex and Mozzie. They go over how they will get into the vault room to steal the music box.
Fowler gets a call from his boss to take down Peter. He goes to meet with Elizabeth to take her business under investigation. Peter gets to Elizabeth’s business and tries to handle the situation, but knocks him in the face and gets pulled from the FBI team.
Neal goes to Peter’s house where admits meeting with Fowler. Fowler somehow rewired Neal’s ankle bracelet so it won’t go off.
Neal meets with Peter and tells him that Fowler is the reason behind why his ankle bracelet is not going off.
At the party, Alex meets with Neal and tells him where the music box is hidden. Neal makes his move and steals the music box. All the security is after him when Alex comes and takes the music box and leaves Mozzie and Neal with just a card to narrowly escape.
Peter meets with Neal the next day and tells him that it isn’t over yet - he still has something in play.
Later that day, Alex shows up at Neal’s place with the music box and tells him that she knows he is worth more than what can come out of their encounter.
Neal meets up with Fowler and gives him the music box.
At the FBI headquarters the woman on Peter’s team, agent Baragot, downloads all the information off of Fowler’s computer.
Elizabeth gets home to a bunch of flowers from Neal. He tells her that he wants to make it up with her.
Peter confronts Fowler and he tells him that Neal is deep undercover in the OPR.
Peter rushes after Neal and meets him at the terminal just before he is about to board. You see Kate on the plane waving at Neal. Neal tells Peter that he deserves a shot to be happy and Peter tells him that he will do so much more good staying here.
Neal turns one last time to say something to Peter, but before he does so the plane, with what looks like Kate is still on it, explodes. Ending the first season.