After a string of mysterious incidents occur in the South Pacific, communication is lost to an American nuclear sub in the waters off Guam. Then, contact is lost from the salvage vessel sent to find the missing submarine... it's last report, sighting a huge living creature with dorsal fins, before it disappeared into the murky depths.

General Tachibana, Supreme Commander of the Self Defense Forces, warns his troops that Godzilla could be rising again for another attack on mankind. General Tachibana lost his parents to Godzilla in 1954, and is deeply concerned with the advent of another tragedy. However, after 50 years of silence, the General Staff of Self Defense Forces were so confident with Japan`s readiness, that they dismissed Tachibana`s concerns of imminent disaster. Meanwhile, strange phenomenon start occurring throughout the Japanese islands in spades. Covering the rise in such supernatural occurrences, is a reality television program called "Digital Q" [Kaneko`s reference to the 1966 monster series ULTRA Q]. The show`s main investigative reporter is Yuri Tachibana (Chiharu Niiyama), General Tachibana`s daughter, who has stumbled upon the threads that are tying one such mystery together.

In three separate regions of Japan, Mt. Myoko in Niigata Prefecture, Lake Ikeda in Kagoshima Prefecture, and Fuji Inland Sea -- where supernatural incidents recently occured -- are the very same areas mentioned in the ancient record, "Gokoku Seishu Denki" (Guardianship of the Divine Beasts). It is these areas where the said beasts would be hibernating. According to the ancient text, "In ancient Japan, there existed Baragon, Mothra, and King Ghidorah, three monsters otherwise known in legends of the `Shiro-inu` (White Dog) or the `Yamata-no-Orochi` (Eight-Headed Serpent), the basis for the legends found in the `Kojiki.` The ancient Royal Court repelled them, and rendered them into hibernation for a thousand years, to serve as guardians to hearten their souls."

While unraveling the pieces of the puzzle, Yuri encounters a strange old man named Isayama, who tells her "Godzilla is the embodiment of the vengeful souls lost in the Pacific War. Therefore, Godzilla cannot be killed by mere weapons. The `Guardian Deities of Yamato` must be awoken!"

The avenging demon, Godzilla, finally comes ashore in Japan. General Tachibana is vindicated -- the combined might of the Self Defense Forces is proven ineffective against the leviathan. In order to protect the sanctity of the land, the "Guardian Deities of Yamato," King Ghidorah, Mothra, and Baragon are called forth. They awaken from their 2000-year slumber, and combine their powers to challenge Godzilla in a duel to the death.

In order to defeat Godzilla, even at the risk of his own life, General Tachibana decides to join the "Guardian Deities" in battle against Godzilla, by operating a secret, ultimate weapon with his own hands. Struck with the realization that her father is fighting alongside the "Guardian Deities" for the sake of the land, Yuri decides to broadcast the battle on live television to the bitter end. Entering the battlefield, she goes beyond the point of no return, and even as death looms for her, she continues her report on the decisive battle.

Who will be the last monster standing?- "Godzilla 2002 in Japan" ...