Jim, the young assistant of the keeper of the Admiral Bembo inn, and his mouse companion Gran(/actor/eiko-masuyama) (Rex in English) are awakened by a rough, one-legged stranger who asks for a room and warns them to keep an eye out for suspicious characters. The warning proves timely: a cloaked band of black-cloaked assassins arrives, and the stranger entrusts Jim with the care of a mysterious casket before facing the intruders. Jim and Gran narrowly escape the danger, hearts pounding as they flee back to the inn in ruins.
When they return, the inn is ransacked, and desperate to make amends they open the casket, hoping to find money to cover the damages. Instead, they uncover a map to a legendary treasure hidden by the infamous pirate Captain Flint. The discovery changes everything, turning a quiet night into a perilous quest.
With a steam-powered barrel boat and a stowaway in tow—the innkeeper’s infant son Baboo(/actor/sachiko-chijimatsu)—Jim and Gran set sail to seek the treasure. Their voyage is cut short when they are captured by the pirate crew led by Silver(/actor/asao-koike) and sold into slavery on Pirate Island. The danger deepens when the monocled Baron(/actor/joji-yanami) steals the map from Jim, hoping to curry favor with the pirate council by presenting it as a prize.
In a damp holding cell, Jim and Gran meet Kathy(/actor/fusako-amachi), the steadfast granddaughter of Captain Flint. The trio escapes, and Jim manages to reclaim the map as the pirate captains gather to scrutinize it. Yet Kathy quickly steals it back, and with no ship to reach the island, she takes on the Baron's offer of transport—a ploy that is swiftly overturned by Silver's own men. The voyage becomes a game of cat and mouse as Silver and his crew attempt to reclaim the map, but Kathy's distrust of their motives and Jim's secret aid repeatedly foil their schemes.
An assault by the pirate chairman nearly costs them everything, but Jim and Gran slip away and manage to render Silver and his crew unconscious with a sleeping potion. Just as they near the island, a violent storm shatters the ship. Jim, Gran, the innkeeper’s baby Baboo, and the walrus guardian Otto(/actor/kosei-tomita) survive the wreck, arriving on the coast just after Silver and Kathy—now their prisoner—have made it ashore.
In a tense exchange, Kathy offers to guide Silver to the treasure’s location in exchange for safety for her friends. Silver plots a double-cross, intending to seize the riches for himself, while Otto holds off the pirates’ advances. The pursuit climbs toward a volcanic peak where the treasure is supposedly hidden, with Jim chasing Silver as he and his monkey helmsman, Spider, ascend toward the crater’s rim.
The turning point comes when Kathy sacrifices the last clue to save Jim’s life. Yet the mechanism described by the pirates does not reveal the treasure immediately; instead, it drains the crater lake, exposing Flint’s sunken ship beneath. With the island’s power restored and the treasure finally visible, the group—including the reformed pirates who had doubted Silver—descends upon Flint’s sunken wreck and unearths the long-lost riches.
The film closes on a hopeful note as Jim and Kathy set sail aboard Silver’s ship, chasing a brighter future together. Behind them, Silver and Spider pursue in improvised log boats, their quarrels echoing across the churning sea as the treasure gleams in the distance. The tale blends friendship, courage, and a dash of clever cunning, inviting viewers to root for the underdogs who outwit fearsome foes and uncover a priceless prize.
