King Ghidorah flew over Japan, leveling cities effortlessly with his gravity beams. As the cosmic terror approached the area, tried to convince her fellow Earth monsters and to cease their fighting and join forces against King Ghidorah. The monsters refused, forcing Mothra to take on King Ghidorah by herself. King Ghidorah blasted the larva with his gravity beams, arousing the anger of Godzilla and Rodan, who finally entered the battle. While King Ghidorah was more powerful than the three monsters individually, he was no match for their combined might, and was beaten into submission and covered in a silken cocoon. As Godzilla pelted King Ghidorah with boulders and threw him off a cliff, King Ghidorah finally retreated and flew back into the void of outer space.

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When astronauts and arrived on the newly-discovered , they encountered an intelligent and technologically advanced alien race called the . The Xiliens' leader, the , explained that his people lived in constant terror due to the attacks of a horrific space monster known as Monster Zero. The Controller showed the two a video feed of the creature, revealing it to be none other than King Ghidorah.

The Controller explained that he knew and drove off King Ghidorah when the monster attacked , and asked that his people be allowed to "borrow" the two monsters to fight off King Ghidorah on Planet X. When the two astronauts returned to Earth and received the support of the world's leaders, the Xiliens revealed themselves, having already been operating on Earth in secret. The Controller apologized for the secrecy, but thanked Earth's leaders and ordered the to transport Godzilla and Rodan to Planet X, with Glenn, Fuji and their superior Dr. Sakurai accompanying them to oversee the mission. When the monsters were placed on Planet X, King Ghidorah flew overhead and attacked them. Godzilla and Rodan joined forces again, and managed to force the space monster to retreat. The Controller remarked that this was a triumphant day for Planet X, and provided Glenn and Fuji with a tape he claimed contained the cure for cancer. The Controller sent the astronauts on their way, keeping Godzilla and Rodan on Planet X.

When the astronauts returned to Earth, they found the tape was actually an ultimatum demanding that Earth surrender to Planet X and become a colony. King Ghidorah had actually been under the Xiliens' control the entire time, and now both Godzilla and Rodan had become their pawns as well. When humanity refused to surrender, the Xiliens released the mind-controlled Godzilla, Rodan and King Ghidorah on Earth to destroy its major cities. Thankfully, Fuji and several Earth scientists discovered a . The device was activated, while the assaulted the Xiliens' hidden base.

The Xiliens lost their control over the monsters, while their forces were defeated by the J.S.D.F. When Godzilla regained consciousness, he woke up Rodan and the two attacked King Ghidorah once again. During the battle, Rodan grabbed Godzilla and carried him in the air, slamming into King Ghidorah and sending all three monsters plummeting into the sea below. After a few moments, King Ghidorah flew out of the water and retreated back to outer space, while Godzilla and Rodan disappeared beneath the waves.

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When the crew of the destroyed the device the were using to control 's monsters, and his fellow monsters assembled near the Kilaaks' base at , preparing to assault it. The Kilaaks proceeded to unleash their trump card, King Ghidorah, to defend their base.

King Ghidorah descended and attacked the Earth monsters, managing to hold his own against several opponents. bit down on King Ghidorah's neck, causing him to take flight and send Anguirus falling to the Earth. King Ghidorah landed and stomped Anguirus into the dust, then reentered battle against Godzilla and his allies. Anguirus, undeterred, got back up and attacked King Ghidorah again. As King Ghidorah battled Godzilla and his allies, landed a devastating kangaroo-kick on his back, knocking him to the ground. Godzilla proceeded to stomp on King Ghidorah's necks, causing him to cough up blood. fired a smoke ring that choked King Ghidorah's remaining head and caused it to fall limp to the ground.

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