| 3x1 | | New Captain | The precinct's new captain makes an unforgettable first impression. Jake and Amy try to keep their budding romance under wraps. |
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| 3x2 | | The Funeral | Another shakeup at the precinct spells trouble for Jake and Amy, while a string of disappointments sends Holt into a downward spiral. |
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| 3x3 | | Boyle's Hunch | A smitten Boyle vows to get a fellow foodie out of prison by proving her innocence. Holt's bid to boost cops' public image sparks a backlash. |
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| 3x4 | | The Oolong Slayer | While Jake and Holt secretly team up to hunt for a serial killer, Amy and Rosa seek revenge for a sexist assignment. |
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| 3x5 | | Halloween III | For their annual Halloween heist, Jake and Holt draft teams and compete to steal a crown. But Amy's divided loyalties leave her out in the cold. |
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| 3x6 | | Into the Woods | Jake and Charles whisk Terry away for an ill-fated camping trip, while Holt helps Rosa with a dilemma, and Amy tries to cash in on an old invention. |
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| 3x7 | | The Mattress | A lovers' spat leads to trouble on the job as Jake and Amy chase down a new street drug. A parking mishap drives a wedge between Holt and Boyle. |
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| 3x8 | | Ava | Jake jumps into action when Terry's wife goes into labor at the precinct. Meanwhile, an Internet outage forces the team to go old-school. |
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| 3x9 | | The Swedes | Tensions flare as Jake and Rosa work a case with two peculiar Swedish cops. Neil deGrasse Tyson drops by to help Gina prepare for a big test. |
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| 3x10 | | Yippie Kayak | A last-minute Christmas shopping trip lands Jake, Gina and Charles in the middle of a "Die Hard"-like hostage crisis. |
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| 3x11 | | Hostage Situation | Boyle tries to recover some sensitive cargo held hostage by his ruthless ex-wife. Amy injures Terry at the worst possible moment. |
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| 3x12 | | 9 Days | An illness leaves Jake and Holt quarantined and delusional as they try to solve a cold case. Terry discovers running the precinct is messy work. |
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| 3x13 | | The Cruise | Jake and Amy embark on a romantic cruise, only to find an old adversary aboard. Holt braces for a visit from his melodramatic sister. |
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| 3x14 | | Karen Peralta | Amy gears up to meet Jake's mother on his birthday, but the celebration takes an unexpected turn. New body cameras prove embarrassing for Boyle. |
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| 3x15 | | The 9-8 | Sparks fly when a neighboring precinct moves in with the Nine-Nine. Jake's reunion with an old partner yields an unhappy surprise. |
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| 3x16 | | House Mouses | Jake persuades Scully and Hitchcock to take over a drug bust so he can help out with a "celebrity" matter. But neither case is what the team expected. |
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| 3x17 | | Adrian Pimento | A cop fresh off an undercover stint with the mob has trouble readjusting to precinct life. Boyle's culinary exploits trigger a janitorial standoff. |
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| 3x18 | | Cheddar | Jake and Amy volunteer to house-sit for Holt, with disastrous results. The chemistry between Rosa and Pimento heats up. |
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| 3x19 | | Terry Kitties | An adorable special delivery reminds Terry of an unsolved case that's haunted him for years. With Jake's help, he sets out to finally crack it. |
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| 3x20 | | Paranoia | A whirlwind engagement sends the gang scrambling to throw twin bachelor and bachelorette parties. But the night of revelry takes an unexpected turn. |
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| 3x21 | | Maximum Security | To root out the crooked FBI agent who targeted Pimento, the team stages an elaborate fake funeral and sends Amy on a risky undercover mission. |
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| 3x22 | | Bureau | With help from an old friend of Holt's, the gang sneaks into the FBI to find dirt on the double agent. An inmate puts Charles in an awkward position. |
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| 3x23 | | Greg and Larry | Jake and the team scour the hospital for a captive Captain Holt, while Amy and Charles book it back to New York to help their friends. |
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