Hiyotoshi Isayama's spirit surveyed the crystal floor of the ancient cave near Mt. Fuji. A stone statuette fell to its side and the transparent ground beneath the solemn spirit cracked and groaned. The radioactive dinosaur Godzilla, the spiritual amalgam of the forgotten spirits of the Pacific War, had defeated the first Guardian Monster, Baragon. The second Guardian Monster, Mothra, was already on her way to do battle with Godzilla. This new creature, lying in wait under the clear stone of the mysterious cavern, would be the third contender to face the tyrannical titan. Isayama's mouth hung low as he watched one of Ghidorah's heads rise several meters above his own. The monster broke through his crystal tomb, ready to do battle with the monstrous menace that threatened the nation. Ghidorah departed from Mt. Fuji and followed Godzilla into Yokohama.

As the second Guardian Monster Mothra grappled with Godzilla in Yokohama, Ghidorah emerged. The majestic moth retreated into the sky to allow Ghidorah a chance to destroy their aggressive adversary. The golden hydra's three heads clamped onto Godzilla, injecting him with severe electrical shocks. The once invulnerable entity finally showed weakness as he lost balance and plummeted into a nearby building. Godzilla countered this effective attack, though, by piercing Ghidorah's middle neck with his razor-sharp teeth. The lacerated neck of the three-headed dragon spilled with blood. As the two titanic terrors sliced through each other's resistant hides, Mothra prepared an ambush; however, her detestable foe merely flicked her aside with his massive tail. Ghidorah continued to inject electrical shocks into Godzilla, but the heroic hydra was lifted and heaved into a building. The Guardian Monster was soon rendered unconscious by Godzilla's scorching thermonuclear ray. As the demonic dinosaur prepared to fire a final blast, Mothra intercepted the full furious force of the attack. With Mothra and Ghidorah down for the count, both of the guardians were seemingly defeated...

Following Godzilla's destruction of the military counteroffensive, a conflagrant Mothra arose from ruins of the once magnificent metropolis. She quietly approached the repugnant reptile from the rear. Godzilla spun to meet Mothra face-to-face. The abhorrent beast reveled in the annihilation of the second Guardian Monster. Godzilla had not yet prevailed over his powerful opponents, however. Mothra's life energy collected together and entered into her immobile ally. Ghidorah, now filled to the brim with an astonishing amount of raw power, awoke revitalized. It had ascended to a new level, and now Godzilla would have to face the full wrath of King Ghidorah!

Taking the power given to him by Mothra in her dying moments, the three-headed deity was transformed. Birthed in illumination, King Ghidorah emerged, thrusting his gigantic wings outward. Rising in shining glory, Japan's last hope stood ready to fight with the terrible titan of man's ignorance.

Godzilla, ready for battle against his reanimated foe, unleashed a blast of his atomic breath at his airborne opponent. The tactic proved futile, however, as the breath collided with a shield obstructed around the guardian monster. Bathed in the glow of Godzilla's ray, King Ghidorah fired back, unleashing a sphere of stored energy at the nuclear terror. The collected energy contacted with deafening effects, as the surrounding waterfront was laid waste by the massive explosion that followed, while Godzilla was thrust into the water.

With his prey submerged, King Ghidorah gave chase. Slamming his body directly into Godzilla, as the two monsters sank beneath the waves. The three-headed deity lashed out with its mammoth jaws, attempting to rend flesh from the bone. His effort was to no avail, though, as two Satsuma class subs arrived to bolster the strike against the nuclear titan. The Satsuma craft unleashed its D-03 missile against Godzilla; however, the beast made use of the situation. Rotating his massive bulk, Godzilla forced his three-headed opponent in the missile's path, as the D-03 blasted a hole in the creature's neck. King Ghidorah reeled in pain, as the King of the Monsters beat back his foe with a blast of his atomic ray.

Fate would not let Japan's defender fall so easily, however, as a piece of the deity's statue plummeted into the water from above, breathing life back into the fallen beast once more. The creature wasted no time, as two humans (Yuri Tachibana and Teruaki Takeda) were falling from a collapsed bridge above. The guardian monster unleashed a powerful gust of breath, which cushioned their decent into the water, as King Ghidorah continued his attack against Godzilla. Rising from the water to do battle with nuclear titan once more, King Ghidorah's body began to glow with a golden hue. The creature then unleashed its most powerful attack, as yellow gravity beams shot out from the creature's maws and struck the water's surface, sending waves churning into the night's sky. King Ghidorah refocused his attack, crashing his body into Godzilla and unleashing the gravity bolts at pointblank range. The attack proved, ultimately, futile though, as Godzilla's dorsal fins surged with the power the guardian monster was showering against it. Godzilla then unleashed the stored energy in a single blast, decimating the three-headed deity once and for all.

After his death, the deity's life essence joined with the other fallen guardians, Baragon and Mothra, as their combined force entered Godzilla's body and dragged the monster down into the depths.