While on vacation on a small island, young Shiina Tamai dives under the water near an old shrine and discovers an unearthly starfish-like creature. She nearly drowns but is rescued by the silent, wide-eyed little animal, who Shiina befriends and names Hoshimaru. To Shiina's surprise and delight, the creature changes shape, lets Shiina stand on him, and the two fly off into the clouds. But what looks to be a young girl's ultimate fantasy soon takes a darker turn as Shiina and Hoshimaru become entangled in a struggle between rival extraterrestrial factions who battle in the skies upon huge alien beasts called Shadow Dragons, with the fate of Earth hanging in the balance.