Mozzie narrowly escapes death and Neal uses his contacts to help Peter find Mozzie's shooter Julian Larssen. However, Larssen manages to blame Peter instead and is released. Suspended from the FBI, Peter enlists the help of Neal, Jones, Diana, Sara, Mozzie and even Elizabeth to run a sting to finally catch Larssen and to clear his name.
An FBI Agent is accused of selling witness locations during criminal trials, and the U.S. Marshals ask Peter and Neal for help tracking down the suspect. But when Peter uncovers the truth behind the plot, he must dive into the world of exotic cars and go on the run with his fellow agent until he can prove the man's innocence.
Peter sends Neal back to school after someone copycats one of his old schemes. Alex returns with some bad news. Diana discovers the music box is hiding something. Peter and Diana set out to find the missing key, which is the last piece of the music box that Alex gives Neal before leaving for Italy. Aidan Quinn guest stars as a criminology professor.
Neal goes undercover as a political "fixer" in order to bring down a corrupt politician. Diana and Peter's lead brings them to an unidentified man who escapes their pursuit. It is also revealed that Peter had Diana keep the music box's location hidden even from Peter himself. Neal begins to suspect that Peter is investigating the plane explosion behind his back.