GODZILLA FINAL WARS
In 2004, endless warfare and environmental pollution has resulted in dangerous kaiju and the Earth Defense Force (EDF) is created to protect the planet. The organization is equipped with the best technology, weapons and soldiers, as well as mutants with special abilities. Godzilla is the EDF's only unstoppable opponent. The EDF's best combat vehicle, the Gotengo, corners Godzilla at the South Pole and buries him under the Antarctic ice, freezing him alive.
Forty years later, the EDF discovers a mummified space monster. The mutant soldier Shinichi Ozaki and the United Nations biologist Dr. Miyuki Otonashi are sent to research it. Shortly thereafter, the two encounter the Shobijin, fairies of the guardian monster Mothra, who reveal that the monster is Gigan, an alien cyborg sent to destroy Earth 12,000 years earlier. They also warn that a battle between good and evil will happen soon and that Ozaki, because of his mutant capabilities, must choose between the two.
Suddenly, kaiju appear in major cities. The EDF attempts to drive them away. The monsters include Anguirus in Shanghai, Rodan in New York City, King Caesar in Okinawa,Kamacuras in Paris, Kumonga in Arizona, Zilla in Sydney and Ebirah near Tokyo. Despite defeating Ebirah, the EDF is unsuccessful in destroying the monsters. After destroying most of the cities, the monsters vanish and an enormous alien mothership appears over Tokyo. The aliens, known as Xiliens, say that they are friendly and have eliminated the monsters. They also warn the Earth about an impending asteroid called Gorath that will impact soon. Because of their seemingly-friendly nature, the UN is disbanded and the Space Nations, an alliance to unite the universe, is organized.
Ozaki, Miyuki, Douglas Gordon (the Gotengo's captain) and several others distrust the aliens. Using research and undercover work, they discover that the Xiliens are actually the ones who unleashed the kaiju; and that they also replaced several members of the EDF with android duplicates. They plan on subjugating humanity to harvest their mitochondria for food. The Xiliens are exposed on television. Opposed to the Xilien commander's decision to subtly take over Earth, his subordinate, the Regulator named X, kills the commander and assumes control of Earth's mutants, except for Ozaki. The kaiju are again released in Earth's major cities. Ozaki, Miyuki, Gordon, and others flee to their secret facility, and the EDF is defeated.
On Mt. Fuji, a hunter, Samon Taguchi, and his grandson, Kenta, discover Minilla, Godzilla's son. They are successful in keeping a low profile and hiding from the Xiliens' assault.
Gordon proposes freeing Godzilla to allow the monster to defeat the other kaiju. Using the Gotengo, the EDF goes to Antarctica while being chased by Gigan. After Godzilla is released from his hibernation, he kills Gigan, and follows the Gotengo. The Gotengo returns to Tokyo, hoping Godzilla will unwittingly defeat the Xiliens. The Xiliens send the controlled kaiju after Godzilla, but he defeats them in short battles. While all of the other kaiju are presumably killed, Godzilla spares Anguirus, Rodan, and King Caesar after defeating them at Mt. Fuji by breaking their controls. The Gotengo and Godzilla arrive at Tokyo, whereupon the Gotengo enters the mothership.
During the battle, Ozaki's friend Kazama destroys the Mothership's shield generator at the cost of his own life. Meanwhile, the asteroid Gorath strikes Godzilla. Monster Xmaterializes and starts to battle him. Gigan, who has now been revived and upgraded, aids Monster X, but Mothra arrives to engage him into battle. Inside the Xilien mothership, the humans confront the Xilien Regulator. Ozaki is revealed to be a "Keizer", an all-powerful being capable of controlling Earth. Deciding to stay with the humans, Ozaki fights the Xilien Regulator, who is also a Keizer. After an extended battle, the humans are victorious and flee the Mothership's destruction.
During their battle, Gigan hits Mothra with a laser beam, causing her to be engulfed in flames. However, Mothra is able to kill Gigan with a kamikaze-style attack after Gigan accidentally cuts off its own head with boomerang saw blades.
With Gigan and Mothra dead, Godzilla continues his battle with Monster X, who mutates into King Ghidorah. King Ghidorah initially has an advantage over Godzilla using gravity beams to overpower him, and it drains Godzilla's power through its bite. Ozaki aids Godzilla by transferring some of his Keizer powers over to the monster. Godzilla, then, rips off two of Ghidorah's heads, throws him into Outer Space, and blows Ghidorah up with his atomic ray. He then turns to attack the Gotengo, but Minilla arrives, along with the hunter and his grandson, and blocks his father from harming the humans, which causes Godzilla to realize that he must forgive mankind. The survivors watch as Godzilla and Minilla head back to the ocean. Right before they vanish into the water, Godzilla turns and lets out one final roar.
During the credits we see that Mothra actually is still alive as she is seen flying back to Infant Island. (From WIKIPEDIA)