Season 4: 2012–13

Neal is contacted again by his old acquaintance and fellow thief Alex, who is being investigated by the FBI in relation to a heist for which Neal is arrested. Peter furthers his covert investigation of "Sam" behind Neal when Neal receives a suspicious package from Ellen delivered by the Marshalls. Alex is in town on more business, which causes some rifts between Peter, Neal, and Mozzie.

 Season 5: 2013-14

Peter is about to be prosecuted for murder, which could end his FBI career even if he were acquitted. Elizabeth urges Neal to save him at any cost. Neal is contacted by the Dutchman, Curtis Hagan (Mark Sheppard), the man he helped Peter convict of forgery in their first case together. Hagan has influence over Peter's prosecutor, and can get the charges dismissed if Neal can make a convincing fake audio confession from James. Neal and Mozzie do this and learn Hagan's price: Neal must steal a collection of gold coins from a secure building. Neal does this with the aid of a device Mozzie has built to spoof the anklet's signal to make him appear to be at home. Neal then learns that the Dutchman has filmed the heist and plans to blackmail him into committing further crimes for him. Peter is promoted to be head of the NYC White Collar Crime office. He gives Neal a new anklet and promises him a new handler from outside the office. Their last case together is to investigate the coin robbery.

Season 6:2014

Peter brings Rebecca in to help locate Neal, who is being held captive by one of her former associates, Jim Boothe. Meanwhile, Jim wastes no time letting Neal know that if he doesn't comply with his demands he'll be pushed down an elevator shaft. Jim has lofty aspirations of joining an exclusive group of thieves, The Pink Panthers, and his entry ticket is the diamond currently held by the FBI. He needs Neal to steal it back. But Neal has a better plan - he thinks the situation calls for a grander gesture, and, for his trouble, he expects something in return. Elizabeth tells Peter that she is pregnant.