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HistoryPlanet X, pleaded for assistance from the people of Earth, as it seemed King Ghidorah, having been driven off Earth the previous year by Godzilla, Rodan, and Mothra, was now assaulting their planet. Mankind allowed the aliens to "borrow" Godzilla and Rodan, and the two monsters were transported to Planet X and were successful in driving Ghidorah away.
Shortly after this, however, the aliens revealed that they had complete control over Godzilla, Rodan, and Ghidorah. They gave humanity twenty-four hours to choose between surrendering themselves to Planet X or being destroyed by the monsters. They finally tired of waiting for an answer and unleashed all three kaiju upon Japan.
Water, very scarce on Planet X, is highly coveted by the Xiliens, and this was the main reason behind their invasion of Earth. The aliens were vulnerable to loud, high-pitched sounds, and humanity used this to defeat them.
The Xiliens were a completely emotionless race, letting their lives be run by computers. Their leader is known as the Controller. Everything on Planet X is numbered, according to the Controller, and King Ghidorah was known as Monster Zero. When the aliens gained control of Godzilla and Rodan, they were known as Monster Zero-One, and Monster Zero-Two.
The Xiliens' spacecraft were capable of traveling one-tenth the speed of light, and could fire explosive laser beams from the domes on their underside. Their ships could also encase targets as big as kaiju inside giant force-bubbles, then use tractor beams to haul them great distances, even from Earth to Planet X. They also possessed laser pistols that were capable of disintegrating a human being. Their greatest power, however, had to be their ability to take control of any creature's mind; they did this to Godzilla, Rodan, and King Ghidorah.
Earth, masking their true intentions with peaceful purposes. They had the ability to control any creature with a certain DNA compound called M-Base, a compound which both the mutant soldiers of M-Force and they can also alter DNA so they can control other creature like the kaiju. They used their control of M-Base to send the monsters on rampages across the globe - Rodan in New York City, Anguirus in Shanghai, Kamacuras in Paris, Zilla in Sydney, King Caesar in Okinawa, Kumonga in Arizona, and Ebirah in Tokai. After allowing them to cause enough damage to their locations, the Xiliens teleported the monsters away, telling the people of the Earth that they rescued them, and want only peace between their planets (Earth and Planet X). They warned humanity of a small run-away planet known as Gorath, saying that unless we aimed all our firepower at it, Gorath would collide with the Earth.
Tension among the Xiliens' ranks soon rose, however. While the leader of the Xiliens, the Controller, wanted to take over the planet through as peaceful means as possible, his second-in-command, X, believed in their superior firepower and technology and wanted to return the monsters to Earth. It was soon discovered that the Xiliens were replacing high political leaders with Xilien clones and that Gorath was not actually going to destroy the Earth. The Xiliens were exposed on national television and with their plan revealed, X shot and killed the Controller, taking command of the invasion from that point on. He explained that the reason for their invasion was to use mankind as a food source - the Xiliens needed mankind's mitochondria to survive. Upon returning to the Mothership, he returned the monsters to Earth, and this time they were assisted by swarms of Xilien fighters. He also activated the Xiliens' ancient weapon - a cyborg kaiju named Gigan.
When Godzilla was awoken to battle the Xilien army of monsters, X was unfamiliar with the beast, and sent the monsters to defeat him. One by one, Gigan, Zilla, Kumonga, and Kamacuras all fell, and even a team attack by Rodan, Anguirus, and King Caesar failed to stop Godzilla. Upon landing in Tokyo, Godzilla simultaneously obliterated Ebirah and Hedorah (Hedorah's location prior to this scene is a mystery, as he is not seen at any other time in the film, leading to the belief he was in the wrong place at the wrong time. However, Hedorah could merely have been making a cameo appearance). Enraged, X sent a secret, last monster, Monster X, into battle via Gorath, in which he was contained. The monster was much more powerful than the previous monsters and overpowered Godzilla numerous times. When Mothra (whom X was also unfamiliar with) arrived in Tokyo, a repaired and upgraded Gigan was sent to destroy her. Monster X and Gigan briefly double-teamed Godzilla before Gigan was destroyed by a kamikaze attack from Mothra. As the two monsters fought, X revealed to the heroes that mutants were the product of interbreeding between humans and Xiliens in the past. He also revealed that he was a Kaiser, an extremely rare type of mutant who is granted super powers due to the fusion of M-base and human DNA. Kaisers are able to control any other life-form by telepathic means if that organism has M-base. Shinichi Ozaki, one of the mutant soldiers, was also a Kaiser, and defeated X in battle. Moments before the Xilien Mothership came crashing down around him, X is seen screaming in anger and agony among the explosions, due to his defeat, after which the Gotengo destroys the ship (and X). Scenes change back to Monster X and Godzilla, who continue to rage in their war for ultimate defeat of the other. After they are both blown away by a massive conflagration when their energy beams collide, Monster X transforms into a hideous monstrosity known as Keizer Ghidorah. For a while, Ghidorah is able to take down Godzilla, and even starts to kill him by draining his life-force. But Ozaki realizes what to do, and transfers his Kaiser energy to Godzilla. Godzilla proceeds to turn the tables on Keizer Ghidorah, tossing him around and then hurling him high into the atmosphere and firing his atomic spiral ray, making Keizer Ghidorah explode.
The Xilien Mothership is immense, and is made of four parts: one massive orb-body, and three claw-shaped ships. These "claw ships" can travel on their own, and have the ability to teleport targets easily. Where the monsters were stored once they were teleported out of their designated cities is unknown, but it was presumably within the main body. The Mothership is protected by a powerful force-field, the generator for which is in the core of the ship itself. The Mothership also houses hundreds of fighters.
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