In the long awaited season premiere of Brooklyn Nine-Nine Season 2 Episode 1, Jake triumphantly returns to the precinct after an incredibly successful undercover operation with the FBI. However, he soon learns that one mobster got away, so he decides to go back undercover to find the missing perpetrator. He enlists the help of Charles, who, in typical Charles fashion, gets a little carried away at times.

Jake also has to deal with his unresolved situation with Amy, having confessed his feelings for her right before going undercover. He realizes that Amy's romantic situation hasn't changed, and then has to decided whether to downplay his feelings and save his pride, or stick with it knowing he has no control over the situation.

Meanwhile, Captain Holt has the rest of the squad on edge, putting them through practice drills for no apparent reason. The squad gets more and more impatient and rebellious as the drills go along. However, unknown to everyone, Captain Holt is nervous about the incoming commissioner, and is trying to prepare his squad for the inevitable scrutiny that they will be under.

Charles and Gina are also trying to figure out how to manage their secret; they slept together 6 months ago and have kept it under wraps. Gina is terrified that Charles, who is unable to keep secrets from Jake, will let the cat out of the bag as soon as Jake returns to the precinct.