In 1885 Shostka, the Mousekewitzes, a Russian-Jewish family of mice who live with a human family named Moskowitz, are having a celebration of Hanukkah where Papa gives his hat to his 5-year-old son, Fievel, and tells him about the United States, a country where there are no cats. The celebration is interrupted when a battery of Cossacks ride through the village square in an anti-Jewish arson attack and their cats likewise attack the village mice. Because of this, the Moskowitz home, along with that of the Mousekewitzes, is destroyed.
In Hamburg, the Mousekewitzes board a tramp steamer headed for New York City. All the mice aboard are ecstatic at the prospect of going to America as there are “no cats” there. During a thunderstorm on their journey, Fievel suddenly finds himself separated from his family and washed overboard. Thinking that he has died, they proceed to the city as planned, though they become depressed at his loss.
However, Fievel floats to New York City in a bottle and, after a pep talk from a French pigeon named Henri, embarks on a quest to find his family. He encounters conman Warren T. Rat, who sells him to a sweatshop. He escapes with Tony Toponi, a street-smart Italian mouse, and they join up with Bridget, an Irish mouse trying to rouse her fellow mice to fight the cats. When a gang of them called the Mott Street Maulers attacks a mouse marketplace, the immigrant mice learn that the tales of a cat-free country are not true.
Bridget takes Fievel and Tony to see Honest John, an alcoholic politician who knows the city’s voting mice. However, he can’t help Fievel search for his family, as they have not yet registered to vote. Meanwhile, his older sister, Tanya, tells her gloomy parents she has a feeling that he is still alive, but they insist that it will eventually go away.
Led by the rich and powerful Gussie Mausheimer, the mice hold a rally to decide what to do about the cats. Warren is extorting them all for protection that he never provides. No one knows what to do about it, until Fievel whispers a plan to Gussie. Although his family also attends, they stand well in the back of the audience and they are unable to recognize Fievel onstage with her.
The mice take over an abandoned museum on the Chelsea Piers and begin constructing their plan. On the day of launch, Fievel gets lost and stumbles upon the Maulers’ lair. He discovers Warren there and that he is actually a small cat in disguise and the leader of the Maulers. They discover, capture and imprison Fievel, but his guard is a reluctant member of the gang, a goofy, soft-hearted long-haired orange tabby cat named Tiger, who befriends and frees him. Angry that he has let Fievel escape, Warren promptly fires him (which he is more than happy to accept, as he never liked Warren or his cacophonous violin playing).
Fievel races back to the pier with the cats chasing after him. There the disguised Warren attempts to extort the mice again to surrender Fievel and their money in exchange for their safety, but when Tony removes Warren’s disguise in front of the mice with the aid of a slingshot, they defiantly refuse. Warren then sets fire to the pier’s entrance in an attempt to burn the mice alive, until Gussie finally orders the mice to release the secret weapon. A huge mechanical mouse, inspired by the bedtime tales Papa told Fievel of the “Giant Mouse of Minsk”, chases Warren and his gang down the pier and into the water. A tramp steamer bound for Hong Kong picks them up on its anchor and carries them away. However, a pile of leaking kerosene cans has caused remnants of the fire Warren had started to ignite the entire pier, and the mice are forced to flee when the human fire department arrives to extinguish it.
During the fire, Fievel is once again separated from his family and ends up at an orphanage. Papa and Tanya overhear Bridget and Tony calling out to Fievel, but Papa is sure that there may be another “Fievel” somewhere, until Mama finds his hat.
Joined by Gussie, Tiger allows them to ride him in a final effort to find Fievel and they are ultimately successful. The journey ends with Henri taking everyone to see his newly completed project—the Statue of Liberty, which appears to smile and wink at Fievel and Tanya, and the Mouskewitzes’ new life in the United States begins.