In the Season 2 premiere of Brooklyn Nine-Nine, Jake returns to the precinct 6 months after beginning his undercover work with the FBI.  The operation ends in a successful sting, until he learns one mobster has gotten away. Unwilling to settle for an incomplete mission, Jake goes back undercover and enlists Charles’ help to track down the missing mobster.

Jake also has to deal with his unresolved situation with Amy. Upon his return to the precinct, he realizes that Amy's romantic situation has not changed. Jake is then faced with the decision to either downplay his interest to save his pride, or to continue being honest about how he feels despite his lack of control over the situation. 

In the meantime, Captain Holt tests the squad’s patience with practice drills. The squad doesn't understand the purpose of these drills, getting more and more rebellious as they go along. Terry finally learns that the captain is nervous about the incoming commissioner, and is trying to prepare his staff for the scrutiny that they're going to face under new leadership. 

Gina and Charles try to figure out how to keep their tryst a secret, especially with Jake's return and Charles's propensity to spill secrets to him.