In order to avoid Earth's impending destruction from an asteroid, the International Solarsystem Development Agency (ISDA) works on the "D-Project", and creates dragons after finding a dragon egg under the ocean.
However, they soon find out that the asteroid is not their only threat, as powerful dragon-like creatures appear on Earth. After witnessing a murder by one of the creatures, Jin Kamishina gets involved in the mysteries of the dragons and becomes a dragon pilot, otherwise known as a "Dragonaut". Helping 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.