A band of samurai sets out to avenge the death and dishonor of their master at the hands of a ruthless shogun.

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.

During a meeting of the Japan Self-Defense Forces (JSDF) for the potential return of Godzilla, Admiral Taizo Tachibana briefs cadets about Godzilla's first attack. A nuclear submarine is reported missing, which is later found to have been destroyed by Godzilla. Tachibana's daughter, Yuri Tachibana, films a docudrama with her crew for BS Digital Q at Mt. Myoko, where a mysterious earthquake randomly ensues. The odd earthquake returns later that night burying a biker gang and leaving one surviving trucker who witnesses the monster, Baragon.

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.

A young man who survives a disaster at sea is hurtled into an epic journey of adventure and discovery. While cast away, he forms an unexpected connection with another survivor: a fearsome Bengal tiger.

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

The world is beset by the appearance of monstrous creatures, but one of them may be the only one who can save humanity.

In the near future, Major Mira Killian is the first of her kind: A human saved from a terrible crash, who is cyber-enhanced to be a perfect soldier devoted to stopping the world's most dangerous criminals.