In 1885, Fievel Mousekewitz, a young mouse, is celebrating Hanukkah with his family in Shostka, Russia. As a gift, Fievel receives a cap that belonged to generations of Mousekewitz mice before him. Papa Mousekewitz regales the family with fables of the Giant Mouse of Minsk and tells them of the prosperity and freedom in a land called America, where there are no cats. Suddenly, Cossacks and their army of cats attack the town, and the mice narrowly escape before their home is burned to the ground. The Mousekewitz family flees to Hamburg, Germany, where they board a ship destined for the U.S. During their long journey, Papa plays violin to entertain his family, but Fievel becomes impatient and grows weary of living on the sea. Exploring the ship, Fievel discovers a barrel of fish and Papa explains there are many kinds of fish in the ocean. Fievel is eager to go on deck to find more fish, but Papa tells him Mama is worried and they return to their community of mouse travelers. The mouse colony sings that there are no cats in America and dance in celebration of their anticipated liberation. One night during a storm, Fievel is swept away from his family by a flood of water inside the ship. When he reaches the foot of a stairwell leading to the top deck, a wave washes several fish aboard. Unable to contain his desire to see more, Fievel throws his cap up the stairway as an excuse to explore the deck while retrieving it. Although Papa anxiously chases after him, Fievel is seized by waves that transform into the shape of an angry monster, and they are separated. When the ship arrives in America, the bereaved Mousekewitz family goes through immigration at Ellis Island while Fievel floats past The Statue of Liberty inside a glass bottle. Washed ashore, Fievel is discovered by Henri, a French pigeon working on The Statue of Liberty, who informs Fievel that he has reached America. Henri takes Fievel in, bathes him, and encourages him to “never say never” and search for his family. Henri’s friend, Chantal, flies Fievel to the Castle Garden Commission of Immigration. Outside, Fievel meets Warren T. Rat, a con man, who convices Fievel he can lead him to his family. Meanwhile, Fievel’s older sister, Tanya, tells her parents that Fievel is alive, but Mama is resolved to accepting his death and assures Tanya that she soon will be, too. Unseen downstairs, Warren T. deposits Fievel at a sweatshop and sells him into child labor. That night, Fievel escapes with the help of Tony Toponi, a street-wise boy mouse who dubs Fievel “Philly.” Before Tony can stop him, Fievel scampers away in search of his family and wanders the streets of New York alone. Hearing a violin, Fievel believes he has found his father, but is disheartened to discover it is only a Victrola. Back on the street, Fievel reunites with Tony, who warns Fievel not to run off again. While Fievel and Tony unknowingly cross paths with Tanya and Papa, Tanya begs Papa to play his violin so that Fievel might hear and find them. Papa refuses, however, insisting that Fievel is gone forever. Tony becomes smitten with a pretty, young Irish mouse named Bridget who speaks before a crowd about fighting back against cats. While Bridget and Tony kiss and stare into each other’s eyes, Fievel earnestly tells the crowd that there are no cats in America, but a cat creeps up from behind and swallows Fievel. On Fievel’s way down the cat’s throat, he clings to its uvula, causing the cat to sneeze and spit him out. In the aftermath of the cat gang attack, Tony tells Bridget that Fievel is looking for his family and she leads them to Honest John, a politician who, she says, knows most of the mice in the city. Bridget, Tony and Fievel find Honest John drunk and adding a dead mouse to his list of “ghost votes” when Gussie Mausheimer, the richest mouse in New York, arrives at the scene and announces she is holding a rally the next day to discuss the community’s cat problems. Bridget asks Honest John if he knows the Mousekewitzes, but he does not, so she takes Fievel home. That night, in separate parts of the city, Fievel and Tanya gaze at the sky and sing, hoping that they will be reunited. The next day at Gussie’s rally, the mice of New York, including the Mousekewitz family, cry out for freedom from cats. Although Fievel sits on stage with Bridget, the crowd obstructs Tanya’s view and she is unable to see him. When the rally is incapable of coming up with a course of action, Fievel whispers an idea in Gussie’s ear and she announces to the cheering crowd that they have a plan. In the early morning fog, the mice march into the abandoned remains of Professor Digitalus’s Museum of the Weird and Bizarre, located on the pier landing of the ship The Star of Hong Kong, and begin engineering its oddities into a secret weapon. Tony and Fievel wake up late, however, and rush to join the other mice. On their way to the pier, Fievel becomes distracted by violin music and follows the sounds into a foreboding sewer. Instead of finding his father, Fievel encounters the gang of cats playing poker, serenaded by Warren T. Rat’s fiddle. Peering at Warren T. from behind a looking glass, Fievel sees him take off his rat nose and discovers that Warren T. is a cat in disguise. After confronting Warren T., Fievel is chased by the cat gang through their sewer lair and nearly escapes, but a paw snatches him back into the manhole. At the pier, Gussie lays out Fievel’s plan. When The Star of Hong Kong sounds its horn at six in the morning and begins its departure, the mice will lure the cats to the pier and release their secret weapon, forcing the cats to retreat and board the ship destined for China. Meanwhile, Fievel is trapped in a birdcage guarded by Tiger, one of Warren T.’s feline lackeys. When Tiger hears Fievel crying, he discovers that Fievel has been separated from his family and begins to sob as well, recounting the loss of his own family. As Tiger sings about his favorite aspects of life, Fievel and Tiger realize that they have a lot in common, even though they belong to enemy species. Tiger releases Fievel from the birdcage and they agree to be friends. An alarm sounds, waking the cat gang, and they chase Fievel to the pier. Screaming to Tony and his mouse friends, Fievel wakes the mouse community at ten minutes to six, initiating their plan ahead of schedule. As the cat gang besieges the museum, the secret weapon begins to launch despite the efforts of Honest John to keep the plan on track, and Gussie faces off with Warren T. He tells Gussie that in exchange for her money and Fievel, he will make sure the cats leave the mice alone, but Fievel announces to the mouse crowd that Warren T. is really a cat. Tony uses a slingshot to knock off Warren T.’s rat nose and ears, and the mice pelt him with dishes and cutlery in disgust. Warren T. retaliates by setting the museum on fire. Just as Honest John manages to halt the secret weapon, both The Star of Hong Kong and the alarm clock set for six a.m. sound their signals. Gussie calls for the release of the secret weapon and the mice scamper to set it in motion. When Fievel finally severs the last rope restraining the secret weapon with a flame, he hits his head on a screw eye and is knocked unconscious. A roaring, mechanical monster, marked “The Giant Mouse of Minsk,” breaks from the museum’s gates amidst exploding fireworks, terrifying the cats and forcing them off the pier and into the water below. Unable to swim, the cats cling to The Star of Hong Kong’s anchor, which hoists them aboard the ship, and they begin their long journey to China. Honest John praises Philly’s plan and the mice sing in celebration that there are no cats in America. Looking on, Tanya asks Papa who Philly is, but he shakes his head in ignorance. While Fievel lies unconscious in the museum, kerosene leaks and intensifies the fire, bringing it to the attention of the mice and the human firefighters, who arrive at the pier and release their hoses. Tony and Bridget search for Fievel and find only his hat, but when Tanya hears them call the name “Philly Mousekewitz,” she suggests to Papa that Fievel’s name was changed to Philly. They chase Tony and Bridget to ask for clarification, but although Tony claims his friend’s name is both Philly and Fievel, Papa doesn’t believe Tony is referring to his son until Mama shows him Fievel’s cap. Meanwhile, Fievel awakens and tumbles through the museum floor in a surge of water from the firefighters’ hoses, safely escaping the burning building. Later, Fievel arrives at Orphan Alley and tells a group of bully mice that he is looking for his family. They convince Fievel that if his family cared about him, they would have found him already, and he becomes despondent. The next morning, however, Fievel is awakened to the sound of Tanya calling his name, but because of his stupor, he is unable to register the hopeful prospect. Riding on the back of Tiger, a search party including Gussie, Mama, Papa, Tony, Bridget and Tanya crosses paths with Fievel but they are unable to see each other in the fog. Finally, Fievel hears Papa’s voice and violin, and realizes they have come for him. As father and son reunite in an ecstatic embrace, Gussie is shocked to find herself hugging her sworn feline enemy, Tiger, but the cat is overwhelmed with joy about his new friendship with the mice. Papa tells Fievel that he never thought he would see him again, but Fievel declares “never say never” and Papa returns Fievel’s cap to his head. On the way home, the Mousekewitz family flies with Henri and Chantal past the newly completed Statue of Liberty, and Lady Liberty gives Fievel a wink. On the horizon, Fievel looks west toward the expanse of the American continent. When he asks to see the rest of America, Henri tells Fievel that he will.