Detective Jake Peralta is a talented, but carefree police detective at Brooklyn's ninety-ninth precinct who, along with his eclectic group of colleagues, are used to having a lax captain around the office. However, when tightly-wound Captain Ray Holt takes over, he is determined to make this dysfunctional group of detectives into the best precinct in Brooklyn.
When Jake is late for roll call, Captain Ray Holt assigns him to a graffiti case that Jake feels is below his level. However, when the culprit turns out to be the Deputy Commissioner’s son, the case becomes a major problem. Meanwhile, Gina’s psychic friend visits the precinct and gets inside Charles.
Jake has a slew of unsolved cases that he can't seem to close, and the other detectives don't want his losing streak to rub off on them. Meanwhile, Holt asks Amy to run lead on the Junior Policeman Program for at-risk youth, and she enlists Rosa and Gina's help. Also, Boyle helps Sergeant Jeffords with a special case he cannot solve.
Much to the team's annoyance, Jake hits on an attractive medical examiner, Dr. Rossi, at a crime scene and holds up the autopsy report. He learns his lesson when Dr. Rossi turns out to be more than he bargained for. Meanwhile, Amy's purse-snatching case is stalled when the sketch artist is out sick, but she discovers that Sgt. Jeffords has hidden artistic talents.
A detective from Special Crimes, takes over Jake’s nearly solved murder case and steals his thunder. Over a few drinks, Jake enlists the precinct to get revenge and find the murder weapon before “The Vulture” does. Across town, Captain Holt and Gina help Terry get re-certified to carry a gun.
It's Halloween night, a busy time of the year for any police precinct. Amy detests the holiday, and is not thrilled when she has to don a costume to go undercover on street patrol with Charles. Back at the precinct, Jake bets Captain Holt that he can steal his Medal of Valor before midnight, which results in him bringing out some costumes of his own.
When Jake makes an arrest without a lot of proof, he only has 48 hours to collect evidence, or else the "perp" will be released. After his unsuccessful interrogation of the suspect, Jake forces his co-workers to spend their weekend helping him crack the case. So, while the team is stuck at the precinct, Charles judges a pie contest between Gina and Rosa, and Holt helps Terry look better in the eyes of his in-laws.
Jake's dream comes true when he gets to spend the day with his hero, Jimmy Brogan, a former crime reporter. But the dream becomes a nightmare when Jake's comments about Holt and the precinct are considered "on the record." Meanwhile, Terry and Charles try to teach Rosa how to be less terrifying on the witness stand.
When Sal's Pizza burns down and the fire marshal quickly assumes that the owner is the prime suspect in the investigation, Jake does everything in his power to prove him wrong, even if it means stepping out of his jurisdiction. Meanwhile back at the precinct, chaos ensues when a computer virus publishes everyone's browser history.
Amy wants to host a Thanksgiving dinner for the entire precinct, but it turns into a holiday disaster when Holt and Jake have to leave to go catch a perp. Boyle steps in to save Turkey Day.
Captain Holt receives death threats and Jake is put in charge of his security, a job he enjoys and abuses as much as he can. Meanwhile, Amy attempts to get the precinct to take a Christmas photo for Holt, but a lack of enthusiasm and Rosa's refusal to smile defeats her efforts. Also, Sergeant Terry Jeffords gets his mojo back.
Jake is interested in one of Rosa's perps, Doug Judy who has information about the "Pontiac Bandit," a car thief whom Jake has been tracking for years. Meanwhile, the station tries to accommodate a scooter-bound Charles' every need when he returns to work, but he proves to be too much to handle. And Captain Holt struggles to find a home for two puppies.
Jake and Amy’s ongoing bet about who can make more arrests comes to a close. Meanwhile, Charles receives the Medal of Valor for getting shot in the line of duty, but the pain medication he is taking causes him to reveal his true opinions about his colleagues.
On his first task back in the field, Terry busts a steroid ring, and in doing so, takes cues from Jake on how to harness his emotions. Meanwhile, Amy and Rosa help solve a breaking-and-entering case at Gina's apartment.
Jake and Amy investigate a string of hotel robberies together, but Jake turns on her when he finds out she may leave the Nine-Nine to work in the Special Crimes unit with “The Vulture”. Meanwhile Captain Holt and Sergeant Jeffords strategize to make the precinct more efficient.
The officers in the precinct head over to Holt’s house to celebrate his birthday, but they wind up making a poor impression on his husband.
Detective Boyle's new romance has upped his swagger, but Jake intervenes before his colleague goes "Full Boyle" and gets too serious, too soon, with his girlfriend. Meanwhile, Rosa and Amy have trouble taking a costumed citizen crime-fighter seriously, and Captain Holt has a new opponent.
Jake's crushing debt finally catches up to him, and he is in danger of losing his apartment, unless Gina can find a way to bail him out. Captain Holt and Sergeant Jeffords hold performance reviews for the entire precinct, and Rosa and Boyle have a run-in with one of the weekend squad officers.
The precinct heads to Tactical Village Day, a mandatory training course in which all regional precincts compete. While there, Amy runs into Teddy, a fellow officer she used to date. Meanwhile, Holt becomes addicted to a game on his phone and Rosa is pissed at Charles for not inviting her to his wedding.
Charles asks Jake to be the best man at his wedding, a role that requires Jake to be supportive in important wedding decisions, ranging from cake tasting to floral arrangements. Meanwhile, Terry, Amy and Gina support each other as they start a new extreme diet and Holt helps Rosa make a sincere apology.
When Jake gets the weekend off, he decides to take on a cold case that everyone thinks is unsolvable, but with the help of Terry, the two try to crack the case once and for all. Meanwhile, Amy plans a romantic trip with Teddy and Gina and Rosa let Charles in on one of their best-kept secrets.
Jake’s investigation of philanthropic civic leader Lucas Wint is shut down by Commissioner Podalski. Still determined to crack the case, Jake enlists Amy and a reluctant Captain Holt to help him uncover more evidence, to help him uncover more evidence, even if it means facing suspension. Meanwhile, Charles is devastated over pre-marital problems with Vivian, and Gina knows just how to cheer him up.