A 15-year-old boy travels back in time—over 1,200 years ago to the Heian period—and faces a war between oni (demons) and humans in the former Japanese capital of Kyoto.

For years, the Niflheim Empire and the kingdom of Lucis have been at war. The empire, having dominated most of the world of Eos, covets the power of the last known Crystal, which is held in Lucis' capital city, Insomnia. In order to protect his people from these advancing forces, King Regis Lucis Caelum CXIII used the power of the Crystal to surround Insomnia with a magical wall. Along with this barrier, Regis assembled an elite military task force known as the Kingsglaive. By drawing their power from the king, the Kingsglaive protect Lucis' borders from the onslaught of the empire and other forces that would do them harm. One such member of the Kingsglaive is Nyx, a man nicknamed "The Hero" by his fellow warriors due to his arrogance and desire to save everyone. However, his pride gets the better of him, causing him to disobey his captain's orders, resulting in a demotion. Now, Nyx spends his days guarding the city gates, but things begin to change once word gets out that Regis plans to sign a peace treaty with their sworn enemies.

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.

By the advent of the 21st century, much of humanity was dead, having been trampled over by a new master, Godzilla. A select few among mankind took to the stars in a spacefaring vessel called the Aratrum in search of "the promised land," the planet Tau-e that could sustain human life. But the migration plan fails, and the remnants of the human race decide to return to Earth. But the distortions in space-time and the distance traveled means that mankind is returning to a completely changed Earth some 20,000 years later. The returnees, led by hero Haruo, prepare to take the fight to Godzilla based on a strategy that has been 20 years in the making. Carried out with the help of two alien species, the Exif and the Bilusaludo, the humans succeed in defeating Godzilla in a costly battle to the death. But the victory is short-lived. Rising from the depths of the planet is a new breed of monster, dubbed "Godzilla Earth." Evolving for 20,000 years, the creature stands 300 meters high, weighs over 100,000 tons and wields such overwhelmingly destructive power that Haruo and company have no choice but to run for their lives. Coming to Haruo's rescue, however, is Miana, a member of an aboriginal tribe called the Houtua. They are the first humanoid people the returnees have encountered. Could they descend from humans? "Our tribal god was destroyed by Godzilla. All that we have left are these eggs. Anyone who has tried to fight or resist him has been drowned in fire," the tribespeople say to Haruo, who responds with: "This is our last hope of recovering our home." Meanwhile, Bilusaludo commander, Galu-gu is elated to discover that the Houtua tribe's arrowheads are made of a nanometal or a self-sustaining metal. It had been developed in the 21st century as an "anti-Godzilla" killer weapon deployed at their decisive battle fought at the foot of Mt. Fuji, but had been destroyed before it could be activated in the form of a "Mecha-Godzilla." The nanometal was its base substance, and proof that the manufacturing plant can still be used.