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 the appearance of a new Gojira (Godzilla), the Japanese government builds a robotic Godzilla from the bones of the original monster that attacked Tokyo in 1954 to stop the beast.

In 2004, Mechagodzilla is undergoing repair modifications after its battle with Godzilla one year earlier. Prime Minister Hayato Igarashi accepts Lead Scientist Yoshito Chujo's choice to replace the Absolute Zero Cannon with a powerful Tri-Maser.

Years after an initial attack of Tokyo in 1954, Godzilla is entrapped under ice in Antarctica after a battle with the original Atragon. In later years, environmental disasters cause the appearance of giant monsters and superhumans, dubbed "mutants", who are then recruited into the Earth Defense Force (EDF) to battle the monsters. An upgraded Gotengo, commanded by Captain Douglas Gordon, battles and destroys Manda (kaiju), but the ship is wrecked in the process and its captain is suspended from the EDF.

Japan is plunged into chaos upon the appearance of a giant monster.