In mid-1992, after the confrontation with Mecha-King Ghidorah, a meteoroid crashes into the Izu–Ogasawara Trench and quietly awakens Godzilla. Six months later, Takuya Fujita, an intrepid explorer, is detained for stealing an ancient artifact. A representative of the Japanese Prime Minister then offers to drop his charges in exchange for letting him travel to Infant Island with his ex-wife, Masako Tezuka, and Kenji Andoh, the secretary of the ambitious Marutomo company. On Infant Island, the trio unearth a cave that depicts a titanic battle between two enormous insects, and their curiosity deepens when they discover a giant egg guarded by a pair of diminutive beings known as the Cosmos—Cosmos #1 and Cosmos #2—who identify the egg as Mothra’s.
The Cosmos recount an ancient civilization that tried to bend Earth’s climate 12,000 years ago, provoking the planet to summon Battra, a formidable, moth-like force that resembled Mothra yet proved uncontainable and destructive. Mothra was sent by the Earth to oppose Battra, who ultimately fell to the struggle. The Cosmos explain that the meteoroid may have unearthed Mothra’s egg and perhaps awakened Battra, who remains resentful of humanity’s meddling with the planet’s delicate balance.
Meanwhile, the Marutomo crew sends a freighter to Infant Island to seize the egg, ostensibly to protect it. As the ship nears its destination, Godzilla surfaces and heads for the newly hatched Mothra larva, while Battra, also in larval form, arrives to join the melee. The clash shifts into the depths, where the ferocity of the combat warps the Philippine Sea Plate and creates a massive fissure that sinks the raging monsters beneath the waves.
Back on land, Masako Tezuka and Takuya Fujita uncover Andoh’s hidden agenda: he has taken the Cosmos to Marutomo’s headquarters, while president Takeshi Tomokane, Marutomo Head Takeshi Tomokane, intends to exploit them for sensational publicity. In Tokyo, Mothra arrives to rescue the Cosmos, only to be met with an aggressive defense by the Japan Self-Defense Forces. Wounded, Mothra journeys toward the National Diet Building and cocooning herself, as Godzilla reemerges from Mount Fuji and Battra frees himself from the Earth’s crust to press toward Japan.
In a dramatic turn, Mothra and Battra attain their imago forms and converge at Yokohama’s Cosmo World to confront Godzilla. Godzilla initially attacks Battra, but Mothra briefly incapacitates the behemoth and comes to Battra’s aid, a mercy that Battra reciprocates. After regrouping, the two moths join forces against Godzilla, recognizing him as the greater threat to the planet. Their alliance drives Godzilla toward the sea, where the colossal trio is finally dragged into the depths.
The tide turns when Godzilla bites Battra’s neck and unleashes an atomic breath into the wound, killing Battra. A fatigued Mothra releases Godzilla and sinks Battra with him, sealing Godzilla beneath the ocean by weaving a mystical glyph from the scales of her wings. Dawn reveals the Cosmos’ revelation: Battra had waited for years to counter a far larger asteroid that threatened Earth in 1999. Mothra had pledged to stop the future catastrophe if Battra were sacrificed, and with that promise fulfilled, Mothra and the Cosmos depart Earth as humanity watches the horizon, bidding farewell to a fragile balance restored for now.
