Communication with an American atomic submarine is lost in the waters off the island of Guam. A vessel is then sent out to try and find the missing sub; however, the reconnaissance craft meets the same fate, although it's able to report a sighting of a huge living creature living in the murky depths before being destroyed. A report which sends some in the Self Defense Force into a warning stage, as fear starts to linger that Godzilla could be rising again for another attack on humanity.

Meanwhile, a strange phenomenon starts to occur throughout the Japanese islands. The bizarre coincidence is that each of the locations where supernatural incidents occur are the very same areas mentioned in the ancient record, "The Guardianship of the Divine Beasts". Vicinities where three legendary beasts are said to be hibernating: Anguirus, Baragon and Varan. According to ancient folklore, the Royal Court repelled the three deities a thousand years ago, forcing them into a state of hibernation to one day serve as guardians to mankind.

Before the relationship between these incidents and legend can be unlocked, though, Godzilla appears on land for the first time in nearly fifty years, and commences an assault on Japanese soil. The SDF amounts an offensive against the creature, utilizing Maser Tanks, but their strike proves ineffective against the nuclear menace. In order to protect the sanctity of the land, the three "Guardian Deities of Yamato" emerge to confront Godzilla. The SDF, seeing this as their only opportunity, begin a plan to support the Guardian monsters as the Gotengo, a multi-purpose battleship which was constructed in secret, enters the fray to join in an all-out attack against Godzilla.

As many know, this screenplay by Shusuke Kaneko was his original pitch for the "Guardian Monster" concept. The idea was approved by producer Shogo Tomiyama, but to Tomiyama's surprise his superiors requested changes to the concept, insisting on the inclusion of Mothra and King Ghidorah into the story. Consequently, this move would cause a great deal of controversy among fans, although the motive was obviously due to character bankability, and after the dismal box office performance of Godzilla vs. Megaguirus (2000) some in the company felt this was the last chance for the Godzilla series in a box office environment that continued to favor non-special effects domestic features. Reportedly, Kaneko agreed after discussing the situation with some of his friends and discovering that most of them weren't familiar with the monsters he was proposing. His compromise, though, was to still include Baragon in the final treatment, although the screenplay was further altered as the Gotengo and Maser Tanks were also dropped in favor of more realistic military weapons.

In regards to the title, the initial concept was given on July 28th, 2000 and the first screenplay was submitted on November 30th, 2000 both with the name: Godzilla X Varan · Baragon · Anguirus: Giant Monsters All-Out Attack. Upon revision, it was resubmitted on January 19th, 2001 as Godzilla X Mothra · Baragon · King Ghidorah: Giant Monsters All-Out Attack before the final draft dropped both the "X" and "Baragon" from the name.

As it turns out, the final product would go on to be the most successful film in the Millennium series at the box office, and convinced Toho to continue the Godzilla series for a few more years.