The great crystal of Atlantis was hidden beneath the city by Kida's father; the crystal is living and keeps Atlantis and its people alive. The crystal grew a conscience when Kida's father tried to use the crystal's power as a weapon and that's what caused Atlantis to sink. Milo and the crew rescue Kida from Rourke. Kida, fused with the crystal, saves the city from being destroyed by lava. Audrey, Mole, Vinny, Sweet, Mrs. Packard and Cookie return to the U.S. with a few treasures. They provide to Mr. Whitmore evidence that they reached Atlantis; Milo sends him a crystal and a thank you note for believing in him and his grandfather. Milo stays in Atlantis and Kida is the next to rule Atlantis. Instead of having the great crystal beneath the city, it's now above the city and the Atlantean civilization is no longer in danger of dying.