Judy finds out the missing animals, still "savage", are being held captive. The Mayor is responsible for their captivity in order to prevent panic, but doesn't know what's causing it, and resists efforts from others to come clean to the public. Judy calls her colleagues who arrive and arrest the mayor. At a press conference she admits that only predators seem to be affected, and without thinking, suggests that they might be reverting to an unevolved state. Nick, a fox, is understandably offended by this, and essentially accuses her of being prejudiced. Dejected, she quits the force and returns home to be a farmer.
While back on the farm, she is apologised to by her childhood bully, a fox, and hears about plants called "nighthowlers" which can cause animals to turn savage. She remembers the weasel she arrested on her first day was stealing them, but didn't realise their effect at the time, and that they're being used to attack animals back in Zootropolis. She races back and with Nick's help tracks down the weasel, who leads her to an underground farm in an old subway carriage. Escaping with the evidence, they call for help.
The carriage is destroyed but they manage to save a gun with the concentrated toxin. The assistant mayor, now mayor, arrives and wants to take the evidence, but suspicious of how she got to them so quickly, Judy resists, eventually realising she was behind the plot from the beginning, wanting to divide the citizens of Zootropolis and keep them in fear of predators. The mayor shoots Nick with the toxin in order to turn him savage so he'll kill Judy, and appears to, before revealing he switched the toxic pellet with a blueberry, and they were just stalling for time so the cops could arrive - they do, and the mayor is arrested. Peace is restored, divisions are healed, and Nick becomes the first fox recruit to the ZPD.