After weeks of working the Vincent Adler case with little to show for it, the team finally gets a break when Sara uncovers what Adler has been hunting: a lost German U-Boat, wrecked off the coast of New York. While the rest of the department searches for Adler, the team tries to track down Alex, who may know more about the submarine than anyone else. But when Adler resurfaces, Peter worries that Alex and the calculating billionaire may be in cahoots.
Hoping for a lead, Neal and Peter head to Alex's last known wherabouts. But Neal's old mentor is one step ahead of them, and they're taken into custody and given a powerful sedative. Coming out of the fog, Neal and Peter find themselves in a warehouse with Alex at their side. The three of them are soon treated to an awe-inspiring sight: the German U-Boat, recovered from the bottom of the ocean. However, the door to the submarine is rigged with enough TNT to level a square block. And guess who Adler thinks should open it?
Meanwhile, Mozzie searches for the sub with his fractal antenna, but it's woefully underpowered. The team slowly comes to the realization that Neal and Peter are missing, but with only Mozzie's antenna and an entire city to search, they seem ill equipped for the job.
Back at the warehouse, Neal and Peter hit a snag. It seems the U-Boat's security measures are run through an Enigma, a code-breaking machine with nearly limitless possible combinations. The task seems hopeless, but through the combined efforts of Neal, Peter and Alex, they disarm the explosives. Little do they realize that what is inside the belly of the boat will change all of their lives forever...