When Godzilla finds a monster to battle, the game switches into a standard side-view fighting segment.

When King Ghidorah suddenly attacks Osaka, the military deploys the Super X II to locate Godzilla, and they use a transmitter to control the mutant dinosaur.

After defeating Biollante, the Super X II rescues Shiragami, it is revealed that the doctor had recovered DNA samples of Godzilla and King Ghidorah and had been experimenting on them to create a serum that enhances the physical attributes of any being.

The aliens travel to the past, where they find and awaken an ancient creature called Bagan and inject him with a sample of the serum, making him just as powerful as Godzilla.

The Super X II disables the transmitter, releasing Godzilla from their control, and the mutant dinosaur returns to the ocean with humanity indebted to him for his aide.

GamePro opined that the visuals and sounds "capture the essence of Godzilla movies" but that the gameplay moves too slow, with extensive time spent on a dull map screen culminating in battles which consist mostly of non-interactive cinemas.

[1] Electronic Gaming Monthly similarly criticized that the map roaming is too slow and boring and the battles are too lacking in interactivity, and additionally complained that frustrating "cheap hits" were too common.