An independent group of researchers called the Godzilla Prediction Network (GPN) actively track Godzilla as he makes landfall in Nemuro. Matters are further complicated when a giant meteor is discovered in the Ibaragi Prefecture. The mysterious rock begins to levitate as it's true intentions for the world and Godzilla are revealed.

In an alternate timeline the original Godzilla is never defeated and repeatedly reemerges to feed on Japan's energy sources. A new inter-dimensional weapon called the Dimension Tide is created with the intent of eliminating Godzilla. However, the new weapon might also serve as a gateway to something far more sinister.

Godzilla has become a distant memory for Japan when the destruction of a US submarine raises alarms for Admiral Tachibana. His estranged daughter Yuri investigates the legend of the guardian monsters, who must rise to protect Japan against the vengeful spirits within Godzilla that seek to destroy both the nation and its people for the suffering they inflicted in the Pacific conflict.

JSDF pilot Akane has a fateful encounter when a new Godzilla emerges in Tateyama. As a countermeasure, a cyborg named Kiryu is constructed from the remains of the original. The machine is discovered to harbor the restless soul of the original monster as Akane must learn to find value in her own life as well.

Mothra and her fairies return to Japan to warn mankind that they must return Kiryu to the sea, for the dead must not be disturbed. However Godzilla has survived to menace Japan leaving Kiryu as the nation's only defense.

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.