In a world of Mobians, chipmunk Sally Acorn from rural Knotholes fulfills her childhood dream of becoming a police officer in urban Mobotropolis. Despite being the academy valedictorian, Sally is delegated to parking duty by Chief Knuckles, who doubts her potential because she is a chipmunk. On her first day, she is hustled by a con artist hedgehog duo, Sonic and Shadow. Sally abandons parking duty to arrest Fang the Sniper, a sniper who stole a bag of crocus bulbs known as Midnicampum holicithias. Knuckles reprimands her, but an bunny, Mrs. Bunnie, enters Knuckle's office pleading for someone to find her husband Antoine, one of fourteen animals who have been reported missing. When Sally volunteers and the city's assistant mayor, Fiona Fox, praises the assignment, Knuckles has no choice but to give Sally the case, stipulating she has forty-eight hours to find Antoine and that she must resign if she fails.
Sally blackmails Sonic into assisting her by covertly recording his confession to tax evasion, having ascertained from photo evidence that Sonic was the last to see Antoine. They track Antoine to a limousine owned by crime boss Mr. Vector, who reveals Antoine went "savage"—reverted to a feral state—and attacked his chauffeur Espio. At his home, Espio mentions Antoine yelled about "Night Howlers" before the attack. Then Espio himself turns savage and chases the pair. Sally saves Sonic by trapping Espio and calls the MPD for help. Upon their arrival, Espio has vanished. Knuckles demands Sally turn in her badge, but Sonic, being saved by Sally earlier, returns the favor by reminding Chief Knuckles that Sally still has ten hours remaining. While leaving the scene, Sonic reveals to Sally that he became a con artist because, as a child, he tried to join the Junior Ranger Scouts, but got rejected by them because none of the scouts trusted him for being a blue hedgehog.
At the City Hall, Fiona offers Sally and Sonic access to the city's traffic cameras. They discover Espio was captured by wolves, whom Sally surmises are the "Night Howlers". They locate the missing Mobians—all gone savage—imprisoned at Cliffside Asylum, where Mobotropolis mayor, Mammoth Mogul, hides them from the public while trying to determine the cause of their behavior. Mogul and the asylum staff are arrested for false imprisonment and Fiona becomes the new mayor. Sally, praised for solving the case, has become friends with Sonic and asks him to join the MPD as her partner. However, she upsets him at a press conference by blaming some Mobian biology for the recent savage behavior, resulting in him angrily rejecting her offer; her comments also incite hateful speech and discrimination against some Mobians throughout Mobotropolis. Wracked with guilt, Sally quits her job and returns home. There, Sally learns the Night Howlers are actually the crocus bulbs Fang stole, and they contain a neurotoxin that has severe psychotropic effects on Mobians. After returning to Zootopia and tearfully reconciling with Sonic, the duo confronts Fang, who, with persuasion from Mr. Vector, tells them the bulbs he stole were for a ram named Finitevous. They find Finitevous in a laboratory hidden in the city subway, developing a drug made from Night Howlers, which he has been shooting at Mobians with a dart gun.
Sally and Sonic obtain the serum as evidence, but before they can reach the MPD, Fiona confronts them in the Natural History Museum and takes the evidence, revealing herself as the mastermind behind a Mobian conspiracy to frame some Mobians as dangerous and savage. Fiona traps them in an exhibition after Sonic refuses to abandon an injured Sally. She then shoots Sonic with the dart gun to make him kill Sally, whilst she summons the MPD for help, but the duo had disarmed the gun by replacing the ammunition with blueberries and baited Fiona into openly declaring her role in the attacks and recorded the confession, just as the MPD arrives on the scene.
Fiona and her accomplices are arrested for their crimes, while Mogul, still in prison, publicly denies knowledge of her plot and states that imprisoning the infected Mobians was a "wrong thing for the right reason". With the cause of the epidemic identified, the predators are cured and Sally rejoins the MPD. Sonic graduates from the Mobotropolis Police Academy as the city's first hedgehog police officer and becomes Sally's partner.
