A door opens, and a golden seal shatters a star. It is the early 21st century. Mankind has lost the battle for planet Earth to Godzilla, and has taken to the stars in search of a new home. But the search ends in vain, forcing them and their alien allies back to Earth. But 20,000 years have passed in their absence, and the Earth is a wholly different place. The planet's flora and fauna now embody and serve Godzilla. Earth is a monster's planet, ruled by the largest Godzilla ever at 300 meters in height. Godzilla Earth. Human protagonist, Captain Haruo, yearns to defeat Godzilla and retake the planet for mankind. There, he meets aboriginal descendants of the human race, the Houtua tribe. The Houtua twin sisters, Maina and Miana, lead him to the skeletal remains of Mecha-Godzilla, an old anti-Godzilla weapon, which to everyone's surprise is still alive in the form of self-generating nanometal. Taken from the Mecha-Godzilla carcass, the nanometals have gradually been rebuilding a "Mecha-Godzilla City," a potential weapon capable of destroying Godzilla Earth. As the strategy develops, a rift forms between the humans and the Bilusaludo, one of several alien races that had joined the humans on their exodus from Earth. Their leader, Galu-gu, believes that the secret to defeating Godzilla lies in the use of superhuman powers – namely, the nanometal integration – but Haruo resists, fearing that in defeating monsters, they must not become monsters themselves. Haruo ultimately uses his means for defeating Godzilla Earth to destroy the Mecha-Godzilla city so as to prevent nanometal assimilation, killing Galu-gu. However, his childhood friend, Yuuko, has been absorbed by the nanometal integration and has fallen into a brain dead coma. The human race, once again, is lost. Metphies, commander of the priestly alien race, Exif, marvels at the miraculous survival of Haruo, he begins to attract a following. The Exif has secretly harbored this outcome as their "ultimate goal." Miana and Maina issue warnings against Metphies, while Haruo begins to question mankind's next move. With no means for defeating Godzilla Earth, mankind watches as King Ghidorah, clad in a golden light, descends on the planet. The earth shakes once again with as war moves to a higher dimension. What is Godzilla exactly? Does mankind stand a chance? Is there a future vision in Haruo's eyes? Find out in the finale.

The world is in the midst of the industrial revolution when horrific creatures emerge from a mysterious virus, ripping through the flesh of humans to sate their never-ending appetite. The only way to kill these beings, known as "Kabane," is by destroying their steel-coated hearts. However, if bitten by one of these monsters, the victim is doomed to a fate worse than death, as the fallen rise once more to join the ranks of their fellow undead. Only the most fortified of civilizations have survived this turmoil, as is the case with the island of Hinomoto, where mankind has created a massive wall to protect themselves from the endless hordes of Kabane. The only way into these giant fortresses is via heavily-armored trains, which are serviced and built by young men such as Ikoma. Having created a deadly weapon that he believes will easily pierce through the hearts of Kabane, Ikoma eagerly awaits the day when he will be able to fight using his new invention. Little does he know, however, that his chance will come much sooner than he expected...

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The Private Aichi Symbiosis Academy was originally a high school for high-class girls. When it became co-ed, the girls, out of fear, asked to be permitted to bring weapons to school. When that was enforced, a five-member vigilante corps-like organization called the "Supreme Five Swords" was also formed. After many generations, the five swords eventually became a group which corrected problematic students, and the academy started proactively accepting such students in order to correct them. Nomura Fudou was sent to this school after being part of a huge brawl. What will he do when the only options he has after enrolling are being expelled from that school or being corrected the way the rest of the male students there were...by being forced to dress and act like a girl!