Godzilla ventured deep into the heart of Tokyo, seeking out an evil from another world. An alien civilization, known as the Xiliens, were attempting to conquer Earth, and Godzilla was the last hope of a dying people. As the gargantuan guardian continued to approach the mothership, an ancient asteroid known as Gorath was approaching the planet at high speed. When Godzilla noticed the meteor, the nuclear behemoth fired his atomic ray. After a few moments, a huge explosion enveloped the celestial body, turning the once shining metropolis into a desolate graveyard. Godzilla stood amidst the wreckage, in the center of an immense crater. As he looked on, he witnessed the arrival of his greatest challenge yet. It was Monster X, and in the vast ruins of Tokyo, the two beasts began to battle savagely, with neither gaining a clear advantage. Luckily, assistance would soon arrive for the forces of good...

Mothra, the winged guardian, arrived to thwart Monster X's attempts to destroy Godzilla. The living tapestry of colors was forced to deal with the Xiliens' newest weapon, however. A fully modified Gigan appeared, and it rendered Mothra unconscious as it began to assist Monster X in Godzilla's defeat. Soon thereafter, Mothra returned to the fray and began to assist Godzilla. She fought Gigan, and in the midst of their battle, both were killed. Only Godzilla and Monster X were left standing.

Beams were exchanged, and the city erupted in a roaring conflagration. Godzilla rose to his feet amongst the flames, as Monster X began to reveal his true identity. In truth, Monster X was a titanic, three-headed space dragon known as Keizer Ghidorah. The final battle for the fate of the planet had only just begun...