When Jake arrives to work at the precinct, announcing that he's arrived on a motorcycle, he finds that Captain Holt is in his chair. And he doesn't look happy. He tells Jake that they are being investigated by internal affairs, but Jake refuses to believe it, saying he knows everyone in the precinct too well.
Later, Jake has his interview with the man from internal affairs, Miller. But Miller is less interested in finding out about the mole than he is about steering clear of germs.
Jake realizes he might be in trouble because he took home some files a while back and never returned them. This might make him a suspect.
Meanwhile, Terry and Rosa go undercover at a silent disco, hoping to find someone doing drugs. Terry is focused on the fact that a nice girl who only wants water went to the same preschool as his twin girls.
Jake tells Amy his dilemma about the files, and she helps him get the files back to the precinct. But in an effort to get the files, they are shocked to catch Charles and Gina sleeping together.
When Jake brings the files back to the precinct, Miller catches him in the act. Worried, Jake visits Captain Holt and they work together to figure out who the Mole could be. After an all-nighter, they come to the conclusion that the mole is Miller, sent as a spy by Deputy Chief Wuntch.
Jake and Captain Holt set the two up, get proof through a gun-shaped flash-drive with a recording device.
Also at the end of the episode, Terry and Rosa get a lead on the drug supplier, and Gina announces to the precinct that she and Charles have been sleeping together.