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, leaving Peter under heavy scrutiny and Neal with the familiar choice: prison or the tracking anklet.
Two months later and it's business as usual. Neal, Peter and Diana are on the hunt for a high profile bank robber known as The Architect.
At the same time, 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. Problem is, the box was logged into evidence after the explosion and they don't think it will sit there for long.
Meanwhile, 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, Peter worries that Kate's death may be affecting him more than he is letting on. And with the department of justice breathing down their necks, one slip up could mean the end of Neal's freedom and Peter's career...