Earth is plunged into conflict again after the Anti-Integration Army tries to dismantle the new world the Shin made. After he crash lands on a mysterious island during a firefight, Shin meets the princess Sara.

Shin finds his life turned upside down when an enemy fighter pilot attacks his peaceful home on Mayang Island. In order to protect his home and his people, Shin decides to pilot an abandoned Variable Fighter.

Mao takes Shin free diving to see her treasure hidden deep within the sea. Meanwhile, the Anti-Unification Alliance and U.N. Military engage in a fierce sea battle for possession of the Bird Human.

Singh and his team are captured by the Nora unit of the Anti-Integration Alliance. Shin and Sara use the power of the Bird People to escape and join the battle for the Protoculture Ruins.

The Mayan island is attacked by the Anti-Integration Alliance, forcing the Bird People to awaken. However, the power of the Bird People proves more powerful than expected. Shin tries to rescue Sara.