Amidst the 20th century, Godzilla, the symbol of humankind's ignorance, emerged to terrorize the world yet again. The Japanese Self Defense Force lured Godzilla to Antarctica, where the military attacked the abomination. Tanks and maser cannons fired with futility on the mountain of flesh. Godzilla destroyed all of his opposition, laying to waste mankind's hopes of annihilating this archfiend. However, humankind wasn't down for the count! Gotengo, a massive aerial battleship, appeared and dueled with the nuclear menace. Gotengo put up a brilliant offensive, but Godzilla was ultimately victorious, or so it seemed... A tremor shook the icy terrain, pulling Godzilla into the pit of the frozen continent. Gotengo took advantage of this wonderful situation, and it fired its missiles at a mountain behind Godzilla. The icy cliffs began to topple and bury the beast. The wretched reptile was frozen, and his reign of terror was over.

Forty years later, a multitude of monsters began to attack the world's largest cities. Millions were killed in the terrible ambush. Suddenly, friends from above, an alien race called the Xiliens, appeared on Earth. In a single stroke, the monsters that were attacking Earth suddenly vanished at the Xiliens' hands, but the beings possessed a terrible secret agenda. Once their plot for world domination was uncovered, the Xiliens once again released their monsters on the world's populous. It was determined that the only possible method by which to save the planet would be to release the terror that slept peacefully in its frozen tomb to the South: Godzilla. The Gotengo was sent to Antarctica to release nuclear menace, but little did they know that a most fierce monster was trailing them.

Gigan, that detestable space cyborg, attacked the Gotengo when it arrived in Antarctica. Luckily, the powerful aircraft managed to destroy the base that had held Godzilla captive for so many years. The king of the monsters, seething with a fiery passion for revenge, emerged. The cybernetic horror fired his cluster beam at the monster. Taking advantage of his preliminary strike, Gigan fired his cables at Godzilla and began to reel him in toward his razor-sharp buzz saw! Unfazed by his apparent doom, Godzilla fired his thermonuclear ray, rending Gigan's head from his shoulders. Godzilla roared in victory, as his foe lay motionless on the icy desert. Godzilla began to leave the site of Gigan's defeat, when the monster noticed Gotengo. It began to follow the craft, firing his atomic ray at his old adversary. Godzilla thought he was still fighting the battle he had waged with Gotengo before he was frozen, unaware of the extreme time lapse. Using this fact to an advantage, the Gotengo began to fly toward Tokyo. If Godzilla could be led to the Xiliens, surely he could destroy them.

Along the way to Tokyo, Godzilla was faced with many enemy monsters under the control of the aliens. First, Godzilla battled the giant lizard Zilla in Sydney, Australia. This monster was easily defeated when it was sent crashing into the Sydney Opera House. Godzilla's deadly nuclear ray followed and the monster was set ablaze. In New Guinea, Godzilla was forced to do battle with the seismic spider Kumonga. The arachnid fired its webbing at his reptilian rival, but Godzilla managed to grab hold to a strand. Since the web that Godzilla held was still attached to the spider, he managed to fling Kumonga thousands of miles away. In Japan, Godzilla fought Kamacuras, the giant praying mantis. Ultimately, Godzilla managed to throw it into a large electrical conductor, killing the beast. Despite every fray that came the monster's way, it lost no steam as Godzilla continued to follow the Gotengo to its destiny in Tokyo.

Godzilla soon found himself facing his greatest challenge yet, though. He arrived in Mt. Fuji, where he faced three monsters simultaneously: Rodan, Anguirus, and King Caesar. The four titans charged at one another, but Godzilla quickly gained the upper hand. Crushing Anguirus' head beneath his foot, the nuclear menace leapt away as Rodan and King Caesar slammed into each other while missing their mark. The battle waged on, as Godzilla managed to slam his tail into Anguirus, sending him on a collision course with Rodan, causing the terrible pterosaur to be sent crashing into the ground. King Caesar retaliated, kicking Anguirus back to Godzilla like a soccer ball! Godzilla avoided the attack, though, and Anguirus was sent toppling onto Rodan. King Caesar's ears stood straight into the air, for its anger was swelling to a boiling point. The mammalian monster charged, but Godzilla grabbed the furry colossus and threw him into a hill, causing him to topple onto Anguirus and Rodan. With the trio of titans defeated, Godzilla roared in victory as it continued to follow the Gotengo.

After Gotengo breached the shell of the Xilien Mothership, Godzilla arose from the depths of Tokyo Bay. The monster made short work of Ebirah and Hedorah as it moved deeper into the city. Meanwhile, the aliens' most powerful weapon, the asteroid called Gorath, had finally breached the Earth's atmosphere. Godzilla fired his breath at the incoming meteor, and the resulting explosion destroyed Tokyo, leaving a crater where the once magnificent metropolis stood.

From within the meteor, a new monster arose. Monster X, as the creature was known, began to battle Godzilla. As they exchanged blows, Mothra appeared! She arrived to assist in the alien race's defeat, but the Xiliens sent a repaired Gigan to do away with the guardian. Gigan sliced Mothra's wing and sent the mammoth moth crashing to the ground. With Mothra seemingly defeated, Gigan proceeded to assist Monster X in Godzilla's annihilation. Mothra, however, rose from the ground and continued to battle with Gigan. The sadistic cyborg sent its spinning razor disks to destroy Mothra, but she reflected them back to their source. The soaring blades decapitated Gigan once more, shortly after his cluster beam set Mothra aflame. The blazing arthropod flew past the decapitated Gigan, causing the demon to explode in a furious ball of fire.

Meanwhile, Godzilla pinned Monster X to the ground, assaulting him with powerful physical blows. Godzilla and Monster X were now battling in a city of flames. They both fired their energy attacks at each other, and this resulted in a massive explosion. As Godzilla slowly rose to his feet, Monster X revealed his true form. He was, in fact, the three-headed space dragon known as Keizer Ghidorah! The malignant monster began to drag Godzilla across the entire city with his gravity beams. Following this terrible onslaught, Keizer Ghidorah began to drain the life force out of Godzilla. However, the Gotengo intervened, and began to assist Godzilla. Using a special energy procured from the Xiliens called "Keizer", Gotengo infused Godzilla with a new power. The revitalized reptile used his newfound strength to destroy two of his opponent's heads. He tossed Keizer Ghidorah into the sky and fired his hyper spiral ray, causing the three-headed demon to erupt in a massive explosion. Godzilla roared in victory!

Godzilla noticed Gotengo, and downed his old enemy with his thermonuclear ray. He was about to finish the aerial battleship once and for all, when an old friend stepped between them. It was Godzilla's son Minilla, and he pleaded with his father to spare the ship. Godzilla listened to his son, and they journeyed out into the sea. Minilla fired an atomic ray into the distance; a symbol that Godzilla's legacy would never end. Godzilla let out one final roar, for his trials and tribulations had finally ended.