On Planet Terra aka Earth, a team of evil Kaiju led by Xenilla aka Spacegodzilla launch an attack on Solgell Island. The island's inhabitants, led by Godzilla Junior, counterattack. Benign Kaiju such as Mothra and Gamera arrive to lend assistance, while the evil Xilians unleash their Kaiju, hoping to finally rid the Earth of the monsters that prevent them from invading. The Gyaos flock arrives, simply wanting to feast on the fallen. The United Nations deploys their mechas: Kiryu, Mechagodzilla 2, and M.O.G.U.E.R.A. to assist the good Kaiju and attempt to contain the fighting.
Anguirus launches himself through the air in his ball mode and rakes the back of Destroyah, forcing her to drop Mothra. Mothra thanks him and flies away. Angered, Destroyah activates her Laser Horn and slams him into the ground. She spreads her wings, moves back a little, and blasts him with her Micro-Oxygen. His armor is strong enough to stop him from being vaporized, but he is still racked with pain and blasted about 1,000 feet back, leaving a trench. Anguirus lays dazed on his back with his soft belly exposed. Destroyah cackles and marches forward, eager to gut him with her Laser Horn. Before she can reach him, Mothra blasts her in the face with lightning from her antennae, knocking her back. As Anguirus gets up, Mothra flies between them and blasts Destroyah again and again.
Meanwhile, a satellite bearing the black hole-generating device Dimension Tide is prepped. When it was last used in the year 2000, it failed and accidentally summoned the Kaiju Megaguirus to Terra. Plus, the scientists are still not sure what exactly happens to the things it sucks up with its black holes. Regardless, it was kept in service as an ultimate last resort. Because of the mass concentration of Kaiju on Solgell Island, the Global Defense Force orders it prepped and ready to fire.
As torrents of rain fall, Godzilla Junior battles his older brother Xenilla. Crackling with nuclear energy, they launch themselves at each other, creating a Kung-Fu Sonic Boom that levels the mountainside and sends tons of debris into the air. Godzilla swings his tail and fractures Xenilla's skull, causing him to scream in pain until the injury heals up. Xenilla conjures a crystal club and bashes Godzilla with it a few times until he manages to catch it. They charge up their free hands with energy and throw a punch at the same time. Their fists collide and create another explosion that shatters the club and sends them both flying back with severe burns. They both get up and their injuries heal. As long as they have energy to spare, they will continue to heal. As long as they can heal, they can fight. They both give earth shaking roars, declaring they will not stop until the other is dead.
The pilots of M.O.G.U.E.R.A.: Koji, Kiyoshi, and Yuki, battle a flock of Gyaos and manage to gun them down. They turn to watch Godzilla and Xenilla's battle, knowing they would just get in the way if they tried to interfere. Suddenly, Akane Yashiro, the pilot of Kiryu, contacts them and warns them to evacuate the island, as Dimension Tide is about to fire. They protest that the good Kaiju are still down there, but are overruled. With no way to warn them in time, they reluctantly leave.
The exhausted, bruised, and bleeding Godzilla and Xenilla continue to bash away at each other. Their bodies are generating so much heat that the rain is evaporating before it can reach them and the plant life is catching on fire. Just as the two fire their respective breath weapons and have a mighty beam-struggle, Dimension Tide fires its miniature black hole, and six Kaiju are wiped off the face of the planet.
The stunned remaining Kaiju call a ceasefire and the invaders leave. Humanity mourns the four good Kaiju who were lost and cheers the fact Xenilla and Destroyah are gone. Little do they know that the lost Kaiju have not been destroyed, but moved.
In Equestria, Princess Twilight Sparkle scans the sky with her telescope. Spike asks why she's up at 5:00 AM, and she says she has an uneasy feeling.
Destroyah drags herself out of the river, incredibly weak. As she wonders what happened, she finds her body has become strange; her now fingerless limbs are covered with fur instead of an exoskeleton. The last thing she sees before she loses consciousness are the Cutie Mark Crusaders: Apple Bloom, Sweetie Belle, and Scootaloo, bending over her and asking if she is all right.
