In the last summer of the 20th century, giant monsters began plaguing Earth and humanity is driven to near extinction by one monster that eliminated the others: Godzilla.
In the last summer of the 20th century, giant monsters began plaguing Earth and humanity is driven to near extinction by one monster that eliminated the others: Godzilla. It was at that time that two alien races with ulterior motives, the religious Exif and the technologically advanced Bilusaludo, came to Earth to offer their assistance against Godzilla. But after the Bilusaludos' gambit with Mechagodzilla failed before it be activated, both the aliens and humanity were forced to abandon Earth and emigrate to Tau Ceti e via the Aratrum. Among the humans is Haruo Sakaki, who bore a seething hatred towards Godzilla as his parents were killed during the exodus. 20 years later and 11.9 light years away from Earth, a fully grown Haruo believes Tau-e is uninhabitable and locks himself in a shuttle that he threatens to detonate unless the ship's committee resents the order for his grandfather and the elderly to scout the planet. But Haruo fails and is arrested, thrown in a cell where he witnesses the emigration shuttle explode while entering the planet's atmosphere. Provided classified data by Exif priest named Metphies, Haruo anonymously publishes an essay detailing Godzilla's weak points to convince the central committee into returning to Earth once they conclude the unlikelihood of finding another habitable world.
Following the events of ''Godzilla: Planet of the Monsters'', the Aratrum is unable to contact Haruo and the rest after their encounter with the original Godzilla. The Captain orders that if drones do not find survivors by 48 hours, the Aratrum will withdraw from Earth.
Following the destruction of Mechagodzilla City, the remaining Bilusaludo on the Aratrum demand justice for Haruo destroying what they saw as necessary to defeat Godzilla. But the humans disagree, believing Haruo exposed the Bilusaludos' true intentions of assimilating Earth. The Bilusaludos revolt and shut down the Aratrum's engine room, forcing the ship to run on secondary batteries for the next two days. On Earth, Haruo learns from Dr. Martin that Yuko is rendered brain-dead with the Nanometal in her body keeping her alive. He also learned that those treated by the Houtua survived the nanometal's attempt to absorb them, with Methphies deceiving the survivors into believing their survival was divine intervention. Dr. Martin advises Haruo to hide until tensions ease.
２０３０年、千葉県逃尾市。 “何でも屋”な町工場「オオタキファクトリー」の有川ユンは、 誰も住んでいないはずの洋館に気配がするということで調査へ。 空想生物を研究する大学院生の神野銘は、 旧嗣野地区管理局“ミサキオク”で受信された謎の信号の調査へ。 まったく違う調査で、まったく違う場所を訪れた見知らぬ同士の2人は、 それぞれの場所で同じ歌を耳にする。 その歌は2人を繋げ、世界中を巻き込む想像を絶する戦いへと導いていく。 孤高の研究者が残した謎、各国に出現する怪獣たち、紅く染められる世界。 果たして2人は、人類に訪れる抗えない未来＜ゴジラ＞を覆せるのか―。