In 1954, Godzilla attacked Japan. From his attack, mankind found and harnessed G-Energy, an energy source taken from Godzilla. 60 years later, Godzilla appears again to feed on the G-Energy. Godzilla progresses through Japan, fighting off Kaiju that are seemingly attracted to him and destroying G-Generators. Mankind takes information on Godzilla, and it is revealed that since Godzilla's first attack, G-Force has been constructing a Godzilla-like robot. Once all the data on Godzilla is collected, the robot is deployed. This can either be Super Mechagodzilla or Kiryu depending on the player's difficulty. Godzilla defeats the robot, and destroys the last two generators. Godzilla then appears to be returning to the sea. However, the energy he absorbs causes him to enter critical mass, and becomes Burning Godzilla. It is theorized that he will explode and destroy the world. The G-Force Operator suggests freezing him, and freeze tanks are sent out. The Super X3 arrives, but is damaged. Soon after, what appears to be another Godzilla appears, but is also defeated. The Gotengo and Super X3 manage to freeze Godzilla, and Kiryu carries him out to sea. They both sink into the ocean, and humanity begins to rebuild.