Godzilla: Final Wars (2004)

Extensive warfare, nuclear testing and careless science had mutated or awakened great beasts of all sorts. During that period, the frequent occurrence of enormous monsters had become commonplace, and thus, the Earth Defense Force (known in short as the EDF) was established by the nations of the world. The sole purpose of the force was to combat the monsters and hopefully restore peace to the world. During the worldwide wave of monsters, mutant humans with superhuman strength and extraordinary physical capabilities were discovered whose origins or mutations were not yet understood. The EDF realized the potential and effectiveness of the mutants as super soldiers, and established a subdivision known as the M-Organization. Utilizing the mutants' handy physical feats and superior piloting skills, along with the military's best war machines, the threat was slowly subdued and the monsters were slowly, but surely, defeated.

In 1954, the greatest enemy that the EDF faced, Godzilla, first appeared and frequently menaced mankind over the years. While the EDF succeeded in defeating the other monsters, it could never overcome Godzilla. Eventually, the EDF engaged Godzilla in a final showdown in Antarctica, pitting its Type 90 Maser Cannons and advanced warship Gotengo against the monster. Godzilla easily destroyed the Maser Cannons and downed the Gotengo with his atomic breath. It was only with the help of a large earthquake that the crew of the Gotengo was able to finally triumph against Godzilla. The earthquake had caused the ground to split and cave-in beneath Godzilla, causing him to fall into a seemingly bottomless pit. This was followed immediately by an avalanche of ice and rock caused by missiles fired from the Gotengo that buried Godzilla and imprisoned him in an icy tomb.

Decades later, in the year 20XX, peace had been recognized worldwide with the exception of very rare monster attacks. The EDF had easily defeated such threats, and the monster-scare had become a thing of the past. During this time a mysterious mummified monster was found off the coast of Hokkaido and was being suspended by large support cables in the EDF warehouse/hangar and being researched. It was calculated at being 12,000 years old and composed of organic and machine tissue, making it a cyborg. It was also discovered that the monster's D.N.A. contains M Base, which was also found in Earth's mutant soldiers. The two Shobijin fairies reveal the creature's name to be Gigan, an evil monster from space that was sent to wipe out life on Earth, but was subdued by Mothra. They give the mutant, Shinichi Ozaki, a small sword, saying he has an important destiny and that he must choose his fate.

Suddenly a large group of monsters appear simultaneously and attack major cities all over the world. The EDF is dispatched and valiantly attempts to defeat the monsters. Rodan attacks New York City, Zilla attacks Sydney, Anguirus attacks Shanghai, King Caesar attacks Okinawa, Kamacuras attacks Paris, Kumonga attacks Phoenix, Arizona, and Ebirah attacks Tokai.

During the international devastation, an alien race known as the Xiliens appears and captures the monsters. After which they proposed a peaceful union with mankind. They revealed that an asteroid called Gorath was going to collide with Earth unless all weapons were aimed at it. The Secretary, who was considered dead when Rodan attacked his plane, began to pursue a new future with the Xiliens, claiming that the United Nations would become the Space Nations. However, distrust of the Xiliens began to arise. When the Secretary was attacked during an attempted assassination, his blood was analyzed and soon found to not be human. Worse, the image of Gorath displayed by the Xiliens turned out to be nothing more than a hologram. Ozaki feared that the Xiliens were plotting a takeover of Earth, and that many of their leaders could have been compromised. He could only trust one man, Captain Gordon, the one who originally fired the missiles that contained Godzilla.

Doctor Miyuki Otanashi went looking through the files of the Secretary, but was caught by the EDF leader. However, Gordon came in at the last moment and shot the EDF leader, revealing the leader to be an impostor. They brought the corpse of the imposter to the broadcast studio, where the Xiliens were being interviewed on live television. The Secretary was shot, revealing him to also be an imposter. The second-in-command of the Xiliens, known as the Controller, shot his commander, tired of the slow plans of a peaceful takeover. Using his species' control over M-base, he takes control of the mutants, excluding Ozaki, and releases the monsters to resume their attacks on the cities. He also sent out an army of small fighter ships to assist in leveling and decimating human civilization. M-Unit commander Muasaka held off his former command while the others escaped. However, their escape is hindered by Kazama, a fellow mutant, who Ozaki is able to subdue.

In a secret hanger, the Gotengo crew set out on a risky, last resort plan to defeat the Xiliens by releasing Godzilla from Area G. The Controller unleashes Gigan to follow them. They succeed in releasing Godzilla, who battles with Gigan and defeats him by decapitation. Godzilla, thinking he was still battling with the Gotengo, chases after the ship. Godzilla is first led to Sydney, where he defeats Zilla. He then proceeds to defeat Kumonga, in New Guinea, Kamacuras in Manazuru, Anguirus, King Caesar and Rodan next to Mount Fuji, and finally Ebirah and Hedorah in Tokyo Bay. He is finally brought to the Xilien mother-ship. The Gotengo attempts to destroy the mother-ship, but its shields are too strong and the Gotengo is soon kept busy with fighter ships. Kazama takes a fighter and manages to enter the mother-ship, destroying the generator, which allows the Gotengo to drill through to the core of the ship and attempt to fire the Maser. However, the Xiliens teleport on board and kill all of the non-essential crew-members, bringing Shinchi, Miyuki, Gordon and pilot Reiko Namikawa to the Controller. The Controller reveals that the Xilians want the mitochondria in human cells to survive and were simply demolishing civilization to show humanity its place as "cattle." He also reveals that he and Ozaki are Keizers, a fusion of mutant and human DNA, which is what allowed Ozaki to avoid his control. However, the Controller manages to control Ozaki until he is stopped by Miyuki, who uses the Shobijiin's sword to free him. The Secretary of Defense and the EDF leader are revealed to be alive, having somehow escaped imprisonment. As the humans make their escape, Ozaki battles the Controller, ultimately winning. Going insane, the Controller self-destructs the mother-ship, intent on taking everyone down with him. Ozaki is able to board the Gotengo just as the mother-ship is destroyed.

Godzilla battles a new, final foe known as Monster X, while Mothra battles a rebuilt Gigan. Gigan perishes as Mothra turns the cyborg's own power against him, just as the remaining crew are victorious. Godzilla is still fighting Monster X, who soon transforms into his true form, Keizer Ghidorah, who defeats Godzilla and starts to drain his life force. Ozaki transfers his "Keizer energy" to Godzilla and restores his strength and empowers him. Godzilla destroys two of Keizer Ghidorah's heads and throws him around the ruins of Tokyo. Finally, Godzilla hurls Keizer Ghidorah into the air and fires his red spiral atomic breath, which pushes Keizer Ghidorah into outer space, where he explodes. Godzilla then continues his battle against the Gotengo, using his atomic breath against the ship, forcing it to crash. Godzilla is about to attack the survivors of the Gotengo, but his son, Minilla, manages to calm Godzilla down and convinces him to leave and forgive mankind for their sins. Together, Godzilla and Minilla leave a ruined Tokyo and Godzilla lets out one final roar to commemorate 50 years of destruction.