Captain Haruo Sakaki bears a seething hatred towards Godzilla, which killed his parents during the exodus from Earth. He believes the planet selected for colonization, Tau-e, is uninhabitable and tries to force the ship’s committee to rescind the order to send the elderly, including his grandfather, to scout the planet. Haruo is arrested and then witnesses the exploratory shuttle explode while entering the planet’s atmosphere. He then anonymously publishes a classified essay on Godzilla’s weak points provided by the Exif priest named Metphies. This sways public opinion among the population forcing the central committee into returning to Earth after deciding that they are unlikely to find another habitable world.

The Aratrum arrives in Earth orbit and sends reconnaissance drones to scout the surface which reveal that Godzilla is still alive. Metphies arranges Haruo’s bail and he explains to the committee that Godzilla has a vulnerability. It is an electromagnetic pulse-producing organ in its body which generates an asymmetrical permeable shield making it impervious to all damage except for a short period when the organ recycles. Haruo proposes using that window to crack the shield organ and quickly implant an EMP probe into Godzilla to cause an implosion from the resulting energy buildup. He stresses that close quarters combat would be needed for accurately coordinated attacks in order to find the organ and requests a force of 600 people to implement the plan.

When Haruo and the two battalions reach Earth’s surface, they learn that almost 20,000 years have elapsed due to relativistic effects. Also, Godzilla’s presence on the planet has radically altered Earth’s biosphere. They suffer losses and damage to their landing ships by flying creatures called Servums. The remaining troops mobilize and soon encounter Godzilla. Haruo proceeds with the original plan on his own and attacks Godzilla before Leland intervenes and provoke Godzilla, his death allowing the others to learn Godzilla’s weak point is its dorsal fins. Command falls to Metphies, who promotes Haruo to commander as the human convinces the remaining survivors to continue with the plan and defeat Godzilla.

The group manage to trap Godzilla within a collapsed mountain pass, where they succeed in killing the monster. However, it appears to only be an offspring and the original Godzilla, which has grown to 300m in height, emerges from beneath a nearby mountain and destroys most of the remaining crew. Trapped beneath rubble, Haruo watches Godzilla leave while vowing to kill it before losing consciousness.

In a post-credits scene, Haruo wakes up in a secluded area and sees an indigenous girl standing next to him.