In New York City, sometime after the events of the first film and before the second one, Fievel Mousekewitz and his friend Tony Toponi wander through an abandoned subway and stumble upon the remains of a dead mouse clutching an old treasure map. They bring the map to an archaeologist they know, Dithering, who deciphers it and learns that the map points to an ancient Lenape treasure buried beneath Manhattan, a relic left behind by the pre-colonial inhabitants of the area. He organizes an expedition to locate the treasure, bringing along Fievel, Tony, Tiger, and his assistant Scuttlebutt. The team faces a series of traps and challenges as they press deeper, testing their courage and ingenuity, all driven by the hope of uncovering something that may redefine their understanding of the city beneath the streets.
What they discover shifts the focus from a wealth hunt to a revelation about a living community. The Lenape welcome the surface visitors and explain that they retreated to their hidden village after witnessing the mistreatment of Native peoples by European colonists. The sachem, Chief Wulisso, decides to send his daughter, Cholena, to the surface to observe whether humans have learned to behave with respect and restraint, and to determine if an alliance might be possible.
Back on the surface, Fievel's father and Tony work in a cheese factory run by the shrewd owners [Grasping], [Toplofty], and [O'Bloat]. The workers endure long hours and low pay, while management keeps a tight lid on dissent, aided by the local police chief, Chief McBrusque. The expedition’s return becomes a tool for distraction, as the factory bosses exploit anti-Native sentiment to sow unrest and divert attention from the workers’ grievances.
Scuttlebutt, who is secretly on Grasping’s payroll, relays news of the Lenape village to the factory owners, giving them a pretext to crack down on anyone assisting Cholena. As tensions rise, the owners send out mobs to seize Cholena and anyone aiding her. Fievel and Tony manage to rescue Cholena from the clutches of the authorities, but Dr. Dithering is captured and dragged to the butcher shop for a public show trial.
Papa Mousekewitz and Tiger step in to intervene. They rescue Dithering and reveal to the crowd how the powerful are manipulating fear and xenophobia to keep workers divided. With public sentiment turning, the factory owners flee and order Chief McBrusque to wipe out the Lenape to prevent any alliance from taking root.
The conflict shifts to the Lenape village, where McBrusque, Scuttlebutt, and their allies attempt to press their advantage. The Native community, joined by Fievel, Tony, and Tanya Mousekewitz, hold the line and drive off the assault. The chief provides a strategic tool—a gunpowder bomb—to collapse the tunnel linking the underground village to the outside world. The ensuing struggle crescendos as the bomb is triggered, sending a torrent of water that floods the tunnel and sweeps away the aggressors, who fall into the chasm below.
As the flood recedes, Tony and Tanya find higher ground while Fievel, though carried away by the current, reemerges moments later to a muddy, joyous group embrace with his friends. In the wake of the chaos, Papa forms a workers’ union and the factory owners are compelled to negotiate, facing a united workforce backed by Tiger, who rises to become the new police chief.
Dr. Dithering’s old telescope serves as a fragile bridge between worlds, a reminder of the possibility for cooperation and curiosity to guide better futures. With Cholena and her father slipping back through a hidden door at the foot of the Statue of Liberty, Fievel looks forward to a future where different communities can coexist, hopeful for what lies ahead for all of New York.
