"Dragonaut -the Resonance-" is set in a future where humanity faces extinction due to a catastrophic asteroid collision with Earth. To prevent this, the International Solarsystem Development Agency (ISDA) develops advanced technology, including the creation of dragon-like creatures called Dragons, which are bonded to human pilots known as Dragonauts. These Dragons are essential for humanity's survival, as they possess immense power and are capable of space travel.

The protagonist, Jin Kamishina, is a young man who lost his family in a shuttle accident years prior. Living in isolation, Jin is drawn into the world of Dragonauts when he encounters a mysterious girl named Toa, who is revealed to be a Dragon in human form. Toa forms a deep bond with Jin, and the two become partners in the fight against the impending asteroid threat. However, their journey is complicated by the existence of other Dragons and Dragonauts, each with their own agendas and motivations.

As the story progresses, Jin and Toa uncover secrets about the ISDA and the true nature of the Dragons. The organization's experiments and manipulations come to light, revealing a darker side to their mission. The narrative explores themes of trust, loyalty, and the ethical implications of scientific advancement. Key characters include Gio, a skilled Dragonaut with a tragic past; Kazuki Tachibana, a determined ISDA officer; and Garnet, a Dragonaut who struggles with her own identity and purpose.

The series balances action, drama, and science fiction, with intense battles between Dragons and Dragonauts, as well as emotional moments that delve into the relationships between the characters. The asteroid threat looms throughout the story, creating a sense of urgency and tension. As Jin and Toa grow closer, they must confront not only external enemies but also their own fears and doubts, ultimately striving to protect humanity and find their place in a world on the brink of destruction.