After Bellwether gives Judy and Nick access to the city's traffic camera system and they discover Manchas was captured by wolves, which Judy surmises are the "night howlers". They locate Otterton and the other missing predators imprisoned in an asylum where Mayor Lionheart has been keeping them hidden and trying to determine the cause of their strange behaviour. Lionheart is arrested and Bellwether becomes the new mayor. Judy, praised for cracking the case, asks Nick to join the ZPD and become her partner, which he happily considers. However, Judy then speaks at a press conference and unintentionally upsets Nick by suggesting a biological cause for the recent predator behaviour. Nick refuses her offer and angrily leaves, and a guilt-ridden Judy quits her job amid a wave of fear and protests against predators, a .
Back in Bunnyburrow, Judy learns from her parents and reformed childhood bully, fox Gideon Grey, that "night howlers" are toxic flowers that have severe psychotropic effects on mammals. Judy returns to Zootopia and reconciles with Nick. They find Weaselton and discover that the bulbs he was stealing were night howlers intended for a ram named Doug. Locating Doug at a lab hidden in the subway tunnels, they find him creating a night howler serum which he has been injecting into predators via a . Before they can bring the evidence to the ZPD, Bellwether intercepts them and steals it, revealing herself as the mastermind behind a prey-supremacist conspiracy. Judy and Nick are trapped in a pit by Bellwether's henchrams after Nick refuses to abandon Judy when she is injured. Bellwether calls the police, intending to use the serum to make Nick kill Judy, but Nick has disarmed the weapon by replacing the serum pellets with blueberries, and Judy has recorded Bellwether's confession. The police arrive and arrest Bellwether. Lionheart denies any knowledge of Bellwether's plot, but asserts that he imprisoned the savage predators for the "right reasons."
Judy rejoins the ZPD, and Nick joins to become her partner and the first fox police officer.