A fishing boat is attacked at sea by a gigantic, hairy monster. After examining the sole survivor (Kanji Tsuda), scientific adviser Dr Murakami (Shiro Sano) suspects the culprit is a “Keukegen spectre”, a shaggy supernatural beast from Japanese folklore. The announcement leads reporter Hideo Akihara (Ken Osawa) to a forest shrine dedicated to the Keukegen Geharha, where he finds several worshipers and learns that an ancient seal containing the monster has been broken.

Humanity finally rids themselves of Godzilla, imprisoning him in an icy tomb in the South Pole. All is peaceful until various monsters emerge to lay waste to Earth's cities. Overwhelmed, humanity is seemingly saved by a race of benevolent aliens known as Xiliens. But not all is what it seems with these bizarre visitors. If humanity wishes to survive, they must reluctantly resurrect their most hated enemy, Godzilla.