Twenty years before the story begins, an asteroid on a collision course with Earth destroys Pluto. Because of Pluto's destruction, the asteroid, named Thanatos, becomes temporarily stagnant. Now, to prevent Earth's impending destruction, the International Solarsystem Development Agency (ISDA) works on the "D-Project" and creates the "Dragonaut" after discovering a dragon egg beneath the ocean. This weapon's main purpose is to destroy the asteroid when the time comes. However, they soon realize that the asteroid is not their only threat, as powerful dragon-like creatures, intent on destruction, appear on Earth. After witnessing a murder committed by one of the creatures, Jin Kamishina, a lonely 18-year-old boy who lost his family in a shuttle accident two years ago, becomes involved in the mysteries of the dragons and is chosen as the pilot of the Dragonaut. Assisting him on his journey is Toa, a mysterious girl who saves him from falling to his death after the creature attacks him. As they delve deeper into the mysteries of the dragons, they encounter new friends and enemies, and also begin to develop a closer relationship.