Twenty years prior to the events in the story, an asteroid named Thanatos destroys Pluto, rendering it inactive. Concerned about the potential collision between the asteroid and Earth, the International Solarsystem Development Agency (ISDA) initiates the "D-Project." The project aims to build the "Dragonaut," a weapon capable of destroying Thanatos. The ISDA discovers a dragon egg in the ocean and uses it to create the weapon. However, their mission hits a snag when destructive dragon-like creatures begin attacking Earth. One of these creatures commits a murder witnessed by an 18-year-old named Jin Kamishina, who has already experienced the tragedy of losing his family in a shuttle accident. Jin becomes involved in the dragons' enigmatic world and ultimately becomes the Dragonaut's chosen pilot. Alongside Toa, a mysterious girl who rescues him from a perilous fall during a creature assault, Jin embarks on a journey to uncover the secrets of the dragons. As he gains new allies and enemies, he forms a close bond with Toa.