Season 3 opens with Neal and Mozzie loading a small plane with the crates of unknown contents, attempting to outrun the Feds who were closing in.

The scene switches to four days earlier with Neal facing a five-hour lie detector test care of Peter, who is unconvinced of Neal's innocence in the destruction of the u-boat and the loss of the treasure.

It seems Mozzie was the one who managed to steal the art from Adler using a rerouting technique with the transmitter he built to determine its location. With the treasure in their possession, Neal and Mozzie decide to stage an elaborate but careful plan to move it out of the country.

In the mean time an old acquaintance, David Lawrence, enters the equation, seeking one of Neal's old aliases, Gary Rydell, to smuggle his stolen money out of the country. The case proves a mirror for Neal, who seems to recognize momentarily the choice he is about to make by smuggling the treasure out of the country.

Peter decides to have the piece of the Chrysler building painting that was destroyed in the fire tested for authenticity. Neal and Mozzie catch onto this plan, and scramble to get it replaced with a period replica to fool the authenticator.

Because their smuggling plan is compromised as a result of the Lawrence case, Neal and Mozzie decide to begin selling pieces from the collection in the underground market to fund their next escape attempt.

Unfortunately for them, Peter remains unconvinced of Neal's innocence, and rightly so given the elaborate plan executed to prevent the truth from coming out, covering up the presence of Neal's Chrysler building painting in the fire remains. This continued suspicion, plus a manifest of at least 22 of the paintings from the U-boat proves an asset to Peter, who plans to use the sale of the paintings to nail the thief.