An ancient guardian, Mothra saved the Earth in times past from the monster Gigan. The two monsters battled thousands of years ago over the fate of Earth, and Mothra ended up being victorious over her cybernetic foe. Several millennia passed, and the mummified remains of the cyborg kaiju ended up displayed in an EDF stronghold for further investigation. While confined, the creature is studied by a team of scientists. Among them is Paleontologist Hachiro Jinguji, who makes the startling discovery that the creature, despite hosting advance technology, is in fact 12,000 years old. A sudden voice chimes in to confirm this, as the interior of the EDF lab appears to melt away into a cave. Before the group, that includes Jinguji and Biologist Miyuki Otonashi, two tiny fairies, known as Shobijin, are spotted lying on a small pedestal. The Shobijin explain that Gigan did arrive on Earth thousands of years ago and was fought into submission by Mothra. The fairies then reassure the group that Mothra will retain its role as the Earth's guardian, before the cave dissipates to reveal the interior of the EDF lab again.

Later, after the Xiliens have initiated a series of attacks, Mothra answers the Earth's plea for help and arrives in Tokyo ready to fight. Once there, Mothra attacks the Xilien's latest kaiju, Monster X, who was battling Godzilla. However, the Xilien leader, spotting Mothra's descent into Tokyo, dispatches a repaired Gigan to do battle with its ancient foe. The two kaiju fight fiercely, slamming their bodies into one another in mid-air, until Gigan gains the upper hand by cutting Mothra's wing with his new chainsaw hands. With Mothra apparently in defeat, Gigan turns his attention to Godzilla, and begins slashing at the monster with his new hands, as Monster X holds the nuclear leviathan in place. The pair's advantage is short lived, however, as Mothra comes flying back into the battle, striking down both Monster X and Gigan simultaneously with her wings. Gigan directs his efforts back at Mothra, utilizing more of his upgraded arsenal as he unleashes two, razor like, discs at the winged monster. Gigan's attack proves futile, however, as Mothra effortlessly dodges the two discs. Gigan continues the assault, though, and lets loose with a discharge of his shotgun like laser beam, which ignites his ancient foe into a smoldering fireball. Gigan, pleased with his success, turns his back to the downed moth. However, the cybernetic kaiju made a fatal miscalculation as the two razor discs, malfunctioning due to Mothra's scales, boomeranged back at the kaiju, decapitating Gigan. Then, out of the smoke and flames, a burning Mothra ascended at her foe in her dying breath, colliding with the robotic kaiju and causing an explosion that destroyed the cyborg for good.