Jim, the young assistant of the keeper of the Admiral Bembo inn, and his mouse friend Gran (Rex in English) are one night asked by a rough, one-legged stranger for a room and to watch out for suspicious-looking characters.

Alerted by Gran's unchecked babbling, one of the crew, the monocled Baron, also steals the map from Jim in order to gain captaincy over his own ship by presenting it to the pirates' council.

Silver and his crew try their best to steal the map back during the voyage, but Kathy's distrust and Jim's secret assistance foil the scheme repeatedly.

Just before reaching the island, however, a storm rips the ship apart; Jim, Gran, Baboo, and the baby's self-appointed guardian, the walrus Otto, arrive just after Silver, his crew, and Kathy, now a prisoner of the pirates.

Silver and Spider are swept out into the sea, and the lake drains to reveal Flint's sunken ship, where Jim, Gran, Kathy and the reformed pirates find the treasure.