With the defeat of the Bilusaludo's nanometal city, the destruction of humanity seems inevitable. Worse yet, Captain Haruo Sakaki's refusal to sacrifice his humanity has come under fire from the remaining Bilusaludo troops, who blame him for their defeat. In their darkest moment, the few surviving humans turn to the religion of the Exifs, which promises that devotion is the path to salvation from Godzilla. However, the Exif are not what they seem. As the survivors become more and more zealous in their devotion, Sasaki wonders what exactly the priest Metphies is hiding—especially regarding his relationship with the monster known as Ghidorah.

When Yun Arikawa and his partner, Haberu Katou, investigate a house rumored to be haunted, the last thing they expect is to stumble into a mystery that will soon envelop the entire planet. While measuring strange radio signals, they receive a call from Mei Kamino, a graduate student investigating the same signal and using the equipment their company previously installed. After an odd night, Yun returns to work at Ootaki Factory, a tech company that actually exists to produce Jet Jaguar—a robot that conspiracy theorist Gorou Ootaki has dreamed of creating. However, when flying dinosaur-like creatures known as Rodan are attracted to the strange radio signals, Jet Jaguar seems to be the only force capable of fighting them. As Yun and Mei investigate the Rodans' sudden appearance, more dangerous monsters begin to surface from the ocean—along with enigmatic red dust.

After a desperate battle and many losses, humans finally slay Godzilla—the monster that caused humanity to flee Earth 20 thousand years prior. But the creature Haruo Sakaki's troops killed was not alone; there existed another Godzilla on Earth yet to be defeated. Grievously wounded from the first conflict, Sakaki wakes up in the home of a young girl who is a member of the Houtua tribe. Bearing a shocking resemblance to humans, the Houtua have adapted to survive the changed climate of the planet that had long been abandoned. With most of their resources depleted, the remaining members of Sasaki's special forces struggle with the decision to abandon their mission and their home planet or to fight an improbable battle. Hope is not completely lost however, as the members from the Bilusaludo race of aliens discover remnants of their anti-Godzilla weapon Mechagodzilla. Even with this powerful weapon in their arsenal, victory seems impossible to grasp: Godzilla has spent all this time evolving and preparing to defeat anyone who dares to challenge its superiority.

Unaired episode 11.5 included with the second Blu-ray/DVD volume.