An asteroid is headed for Earth and in order to avoid Earth's impending destruction, the ISDA create the "Dragonaut" after finding a dragon egg under the ocean. This weapon's primary purpose is to destroy the asteroid when the time comes. However, they soon find out that the asteroid is not their only threat, as powerful dragon-like creatures, which are bent on destruction, appear.

After witnessing a murder by one of the creatures, Jin Kamishina, a lonely 18-year-old boy who lost his family in a shuttle accident, gets involved in the mysteries of the dragons and becomes the chosen pilot of the Dragonaut. Helping him on his journey is Toa, a mysterious girl who saves him from falling to his death after the creature attacks him.