Giant monsters began to attack the world's major cities, but one by one, these enormous organisms began to disappear! Massive airborne vessels, never before seen by man, begin to converge with an enormous, spherical spacecraft above Tokyo. From this "Mothership" came the leader of an alien race, called the Xiliens. He explained that his race had destroyed these monsters, and also explained that the world was in great danger from an asteroid called Gorath. This celestial body could be destroyed, if the world would accept their help and lend the aid of their weapons against the meteor.

However, some humans did not trust the Xiliens and began to seek their true intentions. It was discovered that within the hull of the massive Mothership, the monsters that had attacked Earth were being contained! When their plans were discovered, the Xiliens began to destroy the Earth's populace yet again. An all-out invasion, consisting of an array of monsters and an unfathomable multitude of powerful craft, was unleashed on a hapless planet.

In response, the humans released Godzilla from his Antarctic tomb, for this creature was the last hope for a dying world. The raging reptile was led to Tokyo by Gotengo, a massive aerial war-machine, and along the way, Godzilla defeated wave after wave of enemy monsters. When the Gotengo finally reached the Mothership, the hull of the alien vessel was penetrated, and the crew of the Gotengo journeyed deep into the heart of the colossal craft. After a long battle between Ozaki and the Xilien's leader, the Mothership was set to self-destruct. The humans escaped aboard the Gotengo as the entire Mothership exploded, setting Tokyo ablaze and killing everyone aboard. The Xiliens' plans for invasion were finally put to a halt.