The central mystery of "Castle in the Sky" revolves around the true nature of Laputa and Sheeta's connection to it. It is revealed that Sheeta is not just a girl with a magical pendant, but Princess Lusheeta Toel Ul Laputa, the rightful heir to the throne of the ancient civilization. The antagonist, Muska, is also a descendant of Laputian royalty, from a separate branch of the family, which fuels his obsession with finding and controlling the castle.
The climax reveals Laputa's greatest secret: it houses not only beautiful gardens and benevolent robots but also a superweapon of immense destructive capability, powered by the giant Aetherium crystal at its core. Muska successfully seizes control of this power and demonstrates its might by obliterating a portion of the army's fleet. The final twist comes when Sheeta, recalling a spell of destruction taught by her grandmother, realizes that she and Pazu must destroy Laputa to prevent Muska from using its power to dominate the world. By uttering the word "Balse," they trigger the collapse of the castle's technological infrastructure. Muska is blinded by the light and falls to his death. The ending shows that the spell did not destroy the entire island; the giant tree, with its ecosystem and the city's upper gardens, is freed from the technological core and peacefully ascends higher into Earth's orbit, leaving the destructive power behind forever.