After the Earth was destroyed by mysterious alien lifeforms known as the Gauna, surviving remnants of the human race escaped to space in the enormous generation ship Sidonia. Having drifted through space for millennia, the Sidonia found itself once more under attack from Gauna for the first time in a century. Once again facing the threat of extinction, a temporary victory against the Gauna was eked out thanks to the human-Gauna hybrid Tsumugi Shiraui and ace Guardian mech pilot Nagate Tanikaze. 10 years later... The people of Sidonia enjoy a brief respite. Peaceful days pass, during which Tsumugi begins to realize her feelings for Nagate, who is now celebrated as a hero of Sidonia. However, as Captain Kobayashi has always known, as long as the Gauna remain, peace cannot last. The decision is made: a final battle, upon which rests the fate of humanity's last survivors. As the end approaches, will the crew be able to protect those they love?

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.

(Source: Official site)

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.

(Source: Official site)

While looking for the ledgendary Mapman, the last surviving member of the Nomad Star tribe, Lipumira finds him in Tokyo. His name is Gen Tokishima and he is the only one able to get one part of the starmap hidden within the Earth. After retrieving the piece, Gen must make a decision to follow Lipumira in her foolhardy search to find the remaining pieces of the starmap or stay on Earth. He makes his decision, only to find his girlfriend has beaten him to the spaceship as she wants to come as well. Unfortunately, as Gen learns the secret of the starmap, Lipumira's sisters have plans to stop her and will stop her at any cost.