The film opens in 1885 Russia. A family of Russian-Jewish anthropomorphic mice flee human Cossacks and their cats. The Mousekewitz family decide to board a ship heading to the United States, in hope of finding a better life for themselves. They meet other European immigrants from all Europe with similar hopes. Fievel Mousekewitz, the toddler son of the family, is accidentally separated from his family before their arrival.
The film follows both the efforts of Fievel to survive and locate his family, and the troubles experienced by the Mousekewitzes and the rest of the immigrants. Far from a welcoming homeland, New York is revealed to them as a dangerous place.