The prologue of the film acknowledges the events of the Godzilla (1954 film) (using the 1954 Godzilla monster rather than a successor Godzilla), while inventing its own timeline, explaining that the Oxygen Destroyer was never used here and that the capital of Japan was moved from Tokyo to Osaka. The film takes place in an alternate universe with advanced technology, explaining that in 1966, Godzilla attacks the first Japanese nuclear plant in Tokai, Ibaraki, Ibaraki Prefecture. After this, the G-Graspers, a section of Japanese Self Defence Force, was dedicated to fight Godzilla. In 1996, clean plasma energy replaced nuclear energy, but this did not deter Godzilla from attacking. Plasma energy is also banned, due to the fact that Godzilla attacked the original plasma energy Fusion power.

After having escaped the Maze, the Gladers now face a new set of challenges on the open roads of a desolate landscape filled with unimaginable obstacles.