Mama and Papa Mousekowitz say goodbye to their party guests and they all begin cleaning up. Mama insists it is time for bed for young Tanya and Fievel. The kids begin chanting for presents, as they know the Hannukah tradition well. Papa reveals a new babushka for Tanya and a new hat for Fievel. We learn that the hat has been in the Mousekowitz family for three generations. It is too big for Fievel and covers his eyes, but Mama insists he will grow into it. The kids climb into bed while Papa tells the story of the Great Mouse of Minsk who protects the mice from danger. After the story, the family goes to sleep.

Suddenly, Fievel hears something in the distance. Outside the house, we hear mice shouting “The Cossacks!” Mama insists that everyone needs to hide. We see cat-shaped shadows across the walls. Fievel puts on his hat and charges to the door to defend his family. Papa tries to stop him but isn’t fast enough. Fievel stands facing a giant cat hissing and raising his claws to attack Fievel. Mama throws things at the cat which distracts him long enough for Papa to grab Fievel and pull him back into the house. The Cossack cat disappears but Tanya notices that the house is on fire. The cats are trying to burn the mice out of the village. The flames multiply and we see cat-shaped shadows chasing mice across the stage.

The smoke begins to fade leaving the Mousekowitz family standing among the ruins of their village and home.

We shift to the Mousekowitz family in the hold of a ship crossing the Atlantic. Refugee mice from various countries are here as well. Papa solemnly plays the violin. Tanya worries that they should just stay at their home in Russia but Papa insists that everything will be okay as long as they stay together.

The mice in the lower deck begin to tell stories. Papa tells about how his parents were eaten by cats, leaving him an orphan. They sing that there are “No Cats in America.” Mice from around the world compare and compete for who had a worse situation dealing with cats.

A storm brews tossing the mice back and forth across the boat. They all run for cover while Fievel rushes to close the hatch. He gets to the deck and struggles to close it. Papa follows him to the deck telling him to stop. The wind whips Fievel’s hat off his head and Papa catches it while chasing after his son. Another strong gust of wind throws Fievel off balance and over the railing. Papa lunges forward, holding the hat, and Fievel grabs the other end. They remain suspended like this until one more gust from the storm makes Papa lose his balance, and he lets go of the hat. Fievel, still clinging to the hat, falls overboard into the darkness of the ocean.

The Mousekowitz family (minus Fievel) are in a processing line after finally reaching America. We hear other families go through the process of checking in. The Mousekowitz family is heartbroken to be checking in with one less family member.

In the distance, we see a glass bottle wash ashore with a tiny mouse inside. Fievel climbs out of the bottle to safety on the shore of Ellis Island and is greeted by a pigeon named Henri. Henri gives Fievel a quick run-down of America and promises to help Fievel find his family. The pigeon flies Fievel to mainland America and waves goodbye.

At the harbor, crowds rush everywhere and Fievel is confused about where to start. He begins to ask anyone he can find if they have seen his family. Warren T. Rat is smoking a cigar and watching his underling, a cockroach named Digit, count the earnings for the day. Digit asks Warren to quit blowing cigar smoke in his face but Warren reminds him that there are a million cockroaches who want his job if he isn’t willing to do it. Warren bemoans decreasing sales for the day when his cigar smoke reaches Fievel, causing him to cough. Warren greets Fievel and Fievel tells Warren of his missing family. Warren promises to help him earn money so he can find his family and serenades him with thoughts of all the luxury things he will be able to buy for his family. Warren leads Fievel down a dark hallway, and suddenly Fievel realizes what is happening, but it is too late. Warren gently shoves Fievel towards the sweatshop overseer mouse named Moe. Fievel is now expected to work at a sewing machine, and Warren will receive 90% of his salary as a finder’s fee.

In New York, the rest of the Mousekowitz family are settling into a new apartment. Papa comments that the space is a bit smaller than he anticipated and there are a lot of stairs. The landmouse comments that they are lucky to not have to share with another family or two. Mama reminds Papa that they’ve lost so much already; they should be grateful for what they still have.

At the sweatshop, Fievel is in a line of young orphan mice sewing, including Tony who explains that Fievel must work to pay off his debts. Fievel is confused how he already has debt when he just arrived, but Tony explains that they need to pay off the costs of housing and feeding them before they are allowed to leave.

Fievel says he has to go and find his family, but the other mice say there’s no way out from their high tower. Just then, Fievel has an idea, remembering one of Papa’s stories about a maiden with long hair at the top of a tower. He hatches a plan with the orphans to sew all of their fabric scraps together to create a rope that they can use to climb down from the window of their tower. Fievel and the rest of the orphans escape out of the window after tying up Moe the overseer mouse.

Tony asks Fievel what his name is and decides that Fievel Mousekewitz is a mouthful. He declares that he’s going to call him “Philly” instead.

Papa is hurrying the family with a wheelbarrow full of grapes to sell at the market and just misses Fievel as he climbs out the window. The other orphan mice thank Fievel for helping them escape and go on their separate ways. Fievel begins to call for his family when he sees some cheese in a mousetrap. Tony stops him just in time, and the two decide to stick together from them on.

A young mouse, Bridget, enters with a soapbox and some pamphlets. She begins to preach about the great oppression and encourages mice to work together to stand up to the cats. Tony is infatuated with Bridget. Tony falls deeper in love with Bridget, while other mice challenge Bridget’s views, arguing that Bridget is an instigator and she’ll make the cats come after them. Fievel is confused because he thought there were no cats in America. Just then, a cat appears and attacks, dispersing the crowd. The mice all get away, and Tony introduces himself and Fievel to Bridget.

Tony and Fievel tell Bridget that he has lost his family. She suggests they go to Mouseany Hall to meet with Honest John. He knows practically everyone in the city and will surly know where Fievel’s family is. As the trio exit, we see an older orphan mouse exit the tower, having taken all this time to descend the stairs from the sweatshop. The cat reemerges from the shadows and eats the mouse, coughing up his beard afterwards.

At the market, the Mousekowitz family work to sell all of the grapes in their wheelbarrow. They are pleased with their success when a couple of cockroaches approach. The roaches ask for 90% of all of the mice’s earnings in accordance with the Great Compromouse. We learn that the American mice have promised to pay a percent of their profits to the cats in perpetuity and in exchange the cats have promised to not harm any mouse who is employed.

Bridget arrives at Mouseany Hall with Tony and Fievel in tow. Mice are standing in wake to mourn the loss of their friend, Mickey. Honest John, a local politician, recants Mickey’s life which was cut short when he tried to take time off of work to write a novel- a decision that made him fair game for the cats who caught him 2 days later. The mice toast to Mickey as Honest John notices his visitors. Fievel recants his story to Honest John. Honest John explains that if Fievel’s family aren’t voters, then he doesn’t know them yet.

Suddenly, Gussie Mouseheimer, the richest mouse in town, bursts through the door and demands to speak with Honest John. Gussie is upset that the Great Compromouse does not seem to protect them as it once did. Sometimes the cats are harassing the wealthy mice too, which was not in the agreement. Gussie suggests that the working mice should hand over 95% of their pay instead of 90%. Bridget steps in and suggests that all of mice – workers, the wealthy, and politicians – should unite and fight as one against the cats. Fievel says they need to be all together in one place to see and understand as the townspeople did in “The Emperor’s New Clothes,” a story Papa told him. The mice agree to come together in a rally to end the Great Compromouse.

At the Mousekowitz apartment, Papa is still ranting about the atrocities of making a deal with cats. Mama encourages him to calm down but Papa insists that moving to America was not worth losing Feivel and still being haunted by cats. Tanya yells for her parents to stop fighting.

Bridget brings Tony and Fievel back to her apartment. We learn that her parents were killed by a gang of cats just days after they retired. She assures Fievel that she will work to find his family. Fievel worries that he isn’t brave enough to face the cats. Bridget comforts him by saying that no mouse can face a cat alone; that’s why they all need to work together. She tucks him into bed and encourages him to get some sleep.

Back at the Mousekowitz apartment, Tanya and Mama remember Fievel by setting up a small memorial. Tanya asks if there is any chance that Fievel could be alive and if she could go looking for her brother. Mama has a hard time finding the words to say that Fievel is likely not coming back and kisses Tanya goodnight.

From separate apartments, Tanya and Fievel sing “Somewhere Out There.” Fievel rolls over to go to sleep but Tanya has an idea. She writes a note to her parents, slips Fievel’s photo into her coat pocket, and escapes out the door to look for Fievel. We see Moe the overseer telling Warren T. Rat that the orphan workers have escaped and that Philly Moss is a big problem for them.

After intermission, Bridget is studying books and pamphlets. Tony joins her and asks to talk to her and explains that he has always been a mouse living solo without a care in the world but now he is in love with her. Bridget argues that she needs to focus on uniting the mice, but Tony is insistent. Bridget insists that Tony needs a passion outside of their relationship.

In the streets, mice encourage others to attend the rally. Tanya enters asking the crowd if they’ve seen her brother. They recognize the picture as Philly Moss but not Fievel.  Mama and Papa enter in frantic search for Tanya; they rush off. Everyone is just missing each other.

At Mouseheimer Square, a crowd has gathered for the rally. The orphans have gathered the working mice, Gussie has brought the wealthy mice from uptown, and Honest John made sure the downtown mice are in attendance. Gussie takes the stage and announces that they need to end the Great Compromouse. As the crowd gasps, Honest John and Bridget voices their support.

The crowd starts arguing amongst themselves and voicing their distrust for each other and for the speakers on the stage. As the argument grows, Fievel steps in and calls for everyone to stop. He takes the stage and tells his story.

The crowd is moved, and it seems like they’ll get the crowd on their side when Warren T. Rat speaks up from the crowd. He asks what will happen with the extra money if they’re not giving 90% of it to the cats. His question is a trap to sow distrust and begin an argument between Bridget, Gussie, and Honest John. Bridget says that the extra money would go towards worker benefits and social security. Gussie says that that will only make the workers lazy and dependent. Honest John argues that the money should go to the mice that have been there the longest, not to the workers that are overwhelmingly new immigrants. The different groups keep fighting while Warren gloats. The rally has descended into chaos, and Fievel gets separated from Tony and Bridget in the ensuing riot.

Tony and Bridget stop running and debate whether they are safe. Bridget feels guilty for pushing her agenda instead of just helping Philly find his family. She begins to lose hope in her cause and asks to be alone. Tony is left alone on the stage. He realizes that he can he do something to help!

Meanwhile, Tanya’s search for Fievel has brought her to Mouse Chinatown. She sees one of the other orphan workers from the sweatshop. The mouse lets her know through translated Chinese that they know Fievel, he is going by the name Philly Moss, and he is at the rally. They advise Tanya not to go to the rally because it turned into chaos. She wonders if Fievel made any other friends who can help her, and they tell her about Henri the pigeon. Tanya runs off to find Henri for help.

Fievel runs into the same alley where he was once taken by Warren T. Rat and finds all of his sweatshop friends. He tells them that the rally didn’t go very well and the city has started rioting. Fievel is sad that he didn’t see his family there and wonders why they haven’t come looking for him. He starts making a bed so he can stay with the other mice when he starts to hear a violin. He thinks it is his father, so he follows the sound.

Fievel follows the sound all the way to the sewer where he emerges from a tunnel to find cats playing poker around a large table. Cats argue about the game when Warren steps out of the shadows with his violin. If this wasn’t surprising enough, Warren pulls off his fake nose and ears to reveal he is actually a cat! Unable to contain himself, Fievel rushes forward to confront Warren. Everyone stops to look at Fievel, who realizes he is in trouble. The cats seize him and lock him up in a cage hanging high above the ground. With Fievel locked up, Warren discloses his whole plan to the little mouse including that he created the whole plot for the mice to pay the cats for protection as well as skimming part of the mice’s income. Warren puts his disguise back on and they all exit leaving Fievel locked up and Digit counting the earnings. Fievel cries which distracts Digit from his counting. Digit encourages Fievel to keep his head down and follow directions in order to stay alive. Fievel remembers his life in Russia and remembers the community he had with his fellow villagers. Digit remembers a time he was hopeful for the future and sings with a chorus of cockroaches. Digit decides to free Fievel just as the cats return. The roach chorus lifts Fievel onto their shoulders to carry him out of the sewer and free from the cats.

Papa and Mama return to their apartment feeling defeated that they were unable to find their daughter. Papa bemoans his decision to immigrate the family to America. He throws the window open to find Henri the pigeon at the window. This scares the little mice but Henri assures them that he comes with the gift of Tanya. Tanya shares the good news that Fievel is alive and Henri can help them find him. Mama and Papa are unsure but Tanya insists, and the family boards Henri to head back to the rally location.

Bridget arrives to meet with Honest John and Gussie in the street outside the sweatshop. Bridget is reluctant to be there, but circumstances gave her no choice. Warren enters and shares that the city is in chaos. Gussie, Honest John, and Bridget want Warren to ask the cats for more time on their payment so they can get everything under control. Warren says that the cats will want something in return for their help. He says they’ll want the mice to promise to never try to organize again. The mice are about to promise when Tony bursts in and stops them! Tony declares that he now understands Bridget’s fight – that freedom is not only about freedom to do what you want but also is freedom from oppression. Tony whistles and reveals that he brought the whole city of workers with him. They all declare that they no longer believe in Warren’s plan.

Fievel comes running in, pursued by cats. Bridget and Tony are thrilled to see Fievel and Fievel reveals that he was taken prisoner by Warren T. Rat, who is actually a cat! Digit sneaks up behind Warren and pulls off his disguise to everyone’s shock. Warren and the cats start moving forward menacingly towards the mice. But Fievel has a plan! He tells Warren that they’ll get back to work right away, and he guides all of the mice into the sweatshop, leaving the cats outside. We hear the mice all working together and Fievel reveals that they’ve made one giant mouse out of scraps from the sweatshop. The mouse has giant eyes, big teeth, and shoots flames (fireworks), just like the Great Mouse of Minsk. The mice use their contraption to scare and chase the cats away.

Once the cats are gone, the hastily constructed structure collapses into a pile of debris. But a moment later, all the mice emerge and begin to celebrate the eradication of cats in America when they realize that Fievel is missing. The Mousekowitz family lands with Henri and everyone comes to the conclusion that Fievel is Philly. Amongst the debris, they find Fievel’s hat and begin to panic the worst happened. Papa pulls out his violin to play and Fievel digs his way out of the rubble. The family is reunited at last! Fievel re-dons his hat to realize that it finally fits perfectly.

Fievel and Tanya visit Henri at the now completed Statue of Liberty. We see a human family standing at the base of the statue looking hopeful for the future.