With no means for defeating Godzilla Earth, mankind watches as King Ghidorah, clad in a golden light, descends on the planet. The heavens and earth shake once again as the war moves to a higher dimension.

Humanity’s desperate battle to reclaim the Earth from Godzilla continues. The key to defeating the King of the Monsters may be Mechagodzilla, a robotic weapon thought to have been lost nearly 20,000 years ago.

In the distant technological future, civilization has reached its ultimate Net-based form. An “infection” in the past caused the automated systems to spiral out of order, resulting in a multi-leveled city structure that replicates itself infinitely in all directions. Now humanity has lost access to the city’s controls, and is hunted down and purged by the defense system known as the Safeguard. In a tiny corner of the city, a little enclave known as the Electro-Fishers is facing eventual extinction, trapped between the threat of the Safeguard and dwindling food supplies. A girl named Zuru goes on a journey to find food for her village, only to inadvertently cause doom when an observation tower senses her and summons a Safeguard pack to eliminate the threat. With her companions dead and all escape routes blocked, the only thing that can save her now is the sudden arrival of Killy the Wanderer, on his quest for the Net Terminal Genes, the key to restoring order to the world.

In the year 2048, the human race is forced to leave Earth after decades of losing against Godzilla and other giant monsters. They take a twenty-year journey to another planet called Tau Ceti-e, but upon arrival, they discover that the planet has become uninhabitable. As living conditions on their ship deteriorate, a young man named Haruo spearheads a movement to return to Earth and take it back from the monsters. The ship successfully makes the return voyage, but the crew realizes that twenty thousand years have passed, with Earth’s ecosystem having evolved to become centered around Godzilla.