Save the Earth takes place two years after Godzilla: Destroy All Monsters Melee. The story involves mankind getting hold of Godzilla's DNA, known in the game as "G-Cells." The Vortaak learn of this, once again returning to Earth, controlling a vast army of monsters, including their ultimate weapon: SpaceGodzilla. The player faces down many controlled monsters in different locations. In the climax cut-scene, Godzilla confronts SpaceGodzilla in a final duel. Godzilla blasts off SpaceGodzilla's shoulder crystals causing a black hole to form. SpaceGodzilla is sucked in and apparently killed, forcing the Vortaak to retreat while Godzilla lets out a victorious roar, having saved the Earth yet again.

Save the Earth takes place two years after Godzilla: Destroy All Monsters Melee. The story involves mankind getting hold of Godzilla's DNA, known in the game as "G-Cells." The Vortaak learn of this, once again returning to Earth, controlling a vast army of monsters, including their ultimate weapon: SpaceGodzilla. The player faces down many controlled monsters in different locations. In the climax cut-scene, Godzilla confronts SpaceGodzilla in a final duel. Godzilla blasts off SpaceGodzilla's shoulder crystals causing a black hole to form. SpaceGodzilla is sucked in and apparently killed, forcing the Vortaak to retreat while Godzilla lets out a victorious roar, having saved the Earth yet again.