As Godzilla destroys objects such as buildings, G-Energy Generators, and military vehicles, he will increase in size. Some of these stages are timed and the player must destroy all of the Generators before the timer expires. To clear the stage, the player must destroy all of the G-Energy Generators on the map, while also being attacked by G-Force and occasionally a boss. God of Destruction mode (just called 'Destruction Mode' in the Japanese version) consists of the player controlling Godzilla (or other monsters in the PlayStation 4 version) as he attacks certain stages, and is similar to the gameplay of Godzilla Generations. They both sink into the ocean, and humanity begins to rebuild. The Gotengo and Super X3 manage to freeze Godzilla, and Super Mechagodzilla or Kiryu carries him out to sea. Soon after, what appears to be another Godzilla appears, but is also defeated. The G-Force Operator suggests freezing him, and Maser Cannons armed with freezer weapons are deployed. It is theorized that he will explode and destroy the world. However, the energy he absorbs causes him to enter critical mass, and he becomes Burning Godzilla. Godzilla then appears to be returning to the sea. Godzilla defeats the mecha and destroys the last two generators. This can either be Super Mechagodzilla or Kiryu, depending on the player's chosen difficulty. Once all the data on Godzilla is collected, the robot is deployed.

Mankind takes information on Godzilla, and it is revealed that since Godzilla's first attack, G-Force has been constructing a Godzilla-like robot. Godzilla progresses through Japan, fighting off kaiju that are seemingly attracted to him and destroying G-Energy Generators. 60 years later, Godzilla appears again to feed on the G-Energy. From his attack, mankind found and harnessed G-Energy, an energy source taken from Godzilla.

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