Brooklyn Nine-Nine Season 3 Episode 1 picks up where it left off, with the precinct anticipating the arrival of a new captain.  They meet Captain Seth Dozerman (guest star Bill Hader), who has questionable social skills but prides himself on efficiency. He tasks the squad to work harder than they ever have.

Jake and Amy discuss their kiss and their feelings for each other. They decide to date, but to keep it a secret and keep it light. They go on a date, which starts awkwardly but ends with them sleeping together.

The next day, Dozerman finds Jake and Amy making out in the evidence room, but dies from a heart attack before he can fully punish them. This forces the pair to confess their dating status to the rest of the precinct, and Amy decides to break it off because of all the circumstances surrounding them. However, she later has a change of heart and goes back to Jake.

Meanwhile, Holt and Gina are greeted at Public Relations by Madeline Wuntch, who informs Holt that he is not allowed to start any new initiatives until the ones currently in progress are completed. One of said tasks involves naming the pigeon mascot, a task that has been going on for months. Holt asks Madeline to call a truce so that he can actually get work done. However, Madeline continues to bully him and tells him he has to wear the pigeon costume. Gina encourages the captain not to give up.

With Dozerman dead, the precinct is assigned a new captain. To their chagrin, the new captain is The Vulture, their rival from the Major Crimes unit, who promises to be worse to them than he was before.