After the explosive events of the season one finale, Neal and Peter must deal with the fallout. It seems that Agent Fowler has disappeared and Operation Mentor has been covered up. Peter and Diana hope a clue from Fowler's old files will put them on the trail of the person responsible for the plane bombing. But against Peter's wishes, Neal and Mozzie are also looking into the events of the explosion. Whoever wants the music box, they reason, must be the person who killed Kate. Neal and Peter pay a visit to Edward Walker, a wealthy hedge-fund manager. They suspect that Walker may be The Architect, but when the cocky Walker gets into Neal's head. With the department of justice breathing down their necks, one slip up could mean the end of Neal's freedom and Peter's career.
Following their lead from Fowler's files, Peter and Diana stake out a secret meeting in the hope of getting a jump on whoever was responsible for the plane explosion.
Back at the office, Peter briefs Neal on their latest case, a popular state senator named Gary Jennings who may be illegally funneling money into his campaign. Neal quickly earns Jennings's trust, but the only dirt Neal is able to dig up is a tenuous connection to an escort service. Neal sees a way to use the situation to link Jennings to the escort service. But in order to make it work, Diana is going to have to go undercover as a high-class prostitute.
A copycat criminal is on the loose and they are copying the greatest forger of all time, Neal. What Neal doesn't suspect is that they are changing the game up a little and add their own twist to things. Meanwhile, Alex comes back into picture and is in serious trouble. Neal gets a plan that will not only help Alex, but also catch the copycat thief and make both parties happy.
Mozzie is infatuated with a waitress at a local restaurant. She has bigger problems then having the bald headed Mole being infatuated. When he fears that she has been kidnapped, Mozzie relies on the FBI to help him find the girl and joins the forces with the enemy he has always tried to avoid.
A routine bond theft escalates into an attempted murder when Neal is unknowingly hired to kill the assigned insurance investigator.
When a jewel thief is caught, things seem more than they are when she confesses that she only did it under duress from an adoption liaison Luke Donovan. But things get even more tricky when a local mob boss wants to get his hands into it. Meanwhile, Neal gets the FFA black box recording from Mozzie and gets an unintended, but valuable, asset in the process.
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 before it is too late and they discover his secrets. However things get a little bit more complicated then they imagined.
Neal and Peter must go undercover into the world of corporate espionage after a tech company's head researcher is murdered
When Peter and Neal find a vital clue in the mystery of who killed Kate, Neal orchestrates an elaborate con to bring himself face to face with her murderer
When Peter is suspended by the FBI for a crime he didn't commit, he is forced to run a sting with Neal and the gang to catch Mozzie's shooter, and clear his name.
With the mastermind behind Kate's death uncovered, Peter and Neal explore their pasts to gain answers.
When the son of an American diplomat is detained in Burma for a crime he didn't commit, Peter and Neal delve into the exotic but dangerous world of jewelry smuggling to prove his innocence.
Neal meets an old friend of June who may be up to no good.
Neal's old rivalry with Matthew Keller is rekindled when he and Peter pay a visit to the incarcerated conman. Keller has a tip about a forger turned photographer named Jason Lang who may still have his hand in the counterfeit passport game. But in exchange for the help, Keller wants the FBI to halt his transfer to Barksdale Prison, a supermax facility dominated by the Russian mobsters who still have a price on his head.
Peter and Neal must assume each others' identities to uncover a collusion scheme that is causing blackouts in New York.
Neal gets closer to finding out the truth about Kate's death.