A news segment appears, recounting the story of a police officer receiving a mouse instead of the burrito he ordered. Frank O'Sullivan insists the incident was not an accident.
Captain Holt turns off the news segment and explains what really happened -- the officer called in his order with the name Tom, meaning the restaurant had no idea it was a cop who ordered the burrito. He says O'Sullivan contacted him asking to throw his support beyond the union, but Holt refused.
Terry walks into the break room and tells Holt that the uniformed officers just staged a walkout.
The squad discusses the current situation in the break room. Holt assigns Jake and Charles to prove the doctor's notes are fake and Terry and Amy to develop a plan to keep crime down. Holt plans to ask Rosa to help out since it is not an official investigation.
Jake and Charles begin investigating the doctor's notes. Since Charles cannot contract mono, they conceive a plan for Charles to get the same doctor's note to prove it is fake.
Amy and Terry brief Holt on their progress. Terry abruptly leaves the room because he is sick. The other precinct captains offered two detectives each, but it turns out these detectives are just other versions of Hitchcock and Scully.
Charles goes to the doctor to get a note for mono, but the doctor insists on examining him first. He discovers one of Charles's testicles is not healthy, meaning Charles might have cancer.
Rosa arrives at the precinct, but before she continues her work, she discusses payment with Holt. Holt cannot pay her for an unofficial investigation, but all Rosa wants is to take a picture of his tattoo to show Jake, who will pay Rosa.
Amy updates Holt on the Hitchcock and Scully situation. Jake and Charles arrive, but Charles is having a breakdown because of the possibility of having cancer.
The next day, the squad meets in the break room, where Holt updates them on the blue flu and asks for updates. Terry goes home because he is still sick. Charles is still having an existential crisis even though he is still waiting for his results.
Amy asks Scully for advice on how to deal with the Hitchcock and Scullys from the other precincts.
Terry barges into Holt's office. An officer stopped him on his way out because they thought Terry was joining the walkout, so they invited him to a meeting. Terry plans on going to record the officers acknowledging that the blue flu is fake.
Holt calls Peralta to ask for advice on the investigation's name. Jake and Charles are currently staking out the doctor. Charles puts on loud music, even though Jake is trying to keep a low profile. Jake turns off the music and encourages Charles to talk about his feelings. Charles's words make Jake cry.
Rosa and Holt meet in the storage room. She gives him footage of the officer buying a mouse an hour before finding one in his burrito.
Holt invites O'Sullivan to his office to look at the footage. They argue.
At the next break room meeting, Holt decides the police union cannot be reasoned with and asks for updates from the squad. Jake and Charles are both having existential crises, but Amy successfully makes the Hitchcock and Scullys productive.
After the meeting, Terry bursts into Holt's office with proof from the meeting he attended. However, Terry's stomach noises drown out the proof in the audio recording.
Amy goes to Scully to ask for more advice. Scully is FaceTiming Hitchcock. They tell Amy how the other Hitchcock and Scullys tricked her into believing they were patrolling for crime.
Charles and Jake are staking out the doctor again. Charles is still upset over his potential illness, so Jake suggests things they could do in case Charles potentially dies. Charles realizes that there is nowhere else he'd rather be.
The doctor sends Charles his biopsy results. Jake reads them -- Charles has a treatable infection. They get excited over the news, and Jake realizes how the officers got their doctor's notes.
Jake presents the evidence against the officers in Holt's office. Holt swears at O'Sullivan, who finally admits the officers weren't sick. However, now they are because they caught the stomach bug Terry had from the meeting.
The squad finds Holt in a bar after he missed the morning briefing. He's wallowing with Charles's expensive cheese and a bottle of liqueur he would only open when he became commissioner. Holt has given up on changing the NYPD. Holt thinks of another way to end the blue flu.
Holt goes to see O'Sullivan at his office and backs him into a corner, ending the blue flu.
At the next briefing, Holt tells the squad he will use the data collected from the blue flu to change the NYPD. Jake has a photo of Holt's tattoo; it ends up being a decimal point. Later that night, Holt meets up with Rosa and pays her more than what Jake offered. Rosa promises not to tell anyone about Holt's tattoo. The episode ends before we can find out what his tattoo is.