In the year 2204, a submarine examines the body of King Ghidorah, a monster which was said to have fought Godzilla in the 20th century. Then the movie flashes back to modern day Tokyo, where an unidentified flying object (UFO) has been seen flying rapidly with flashing lights in the night sky. The next morning, the general media attempts to make sense of the situation, which determine that this "UFO" may not have been a hoax.
Terasawa, a young Japanese reporter, is covering a story of a dinosaur sighted during Pacific War. Then a spaceship appears in Japan, coinciding with Godzilla's awakening in the ocean. The ship lands, and three humans--Two Western men Wilson and Grenchiko and one Japanese young woman Emmy--come out of the ship and reveal themselves as delegates of nations from the year 2204. They have traveled across time to warn Japan of it's grave future; due to industrialization and nuclear power, Godzilla will reappear and destroy Japan for good (or so the Futurians say). They present a book that Terasawa will write in the future, entitled The Birth of Godzilla, which states the dinosaur he is covering is a "Godzillasaurus", the dinosaur that would become Godzilla after radiation exposure from an American nuclear bomb test after World War II.
Terasawa and several Japanese civilians and military personnel are selected by the Futurians to go back to 1944 and erase Godzilla from history, thus preventing Japan's bleak future. The Futurians place Emmy and an android named M11 in command of the mission. They will pilot a time traveling shuttle named K.I.D.S. to 1944, where they will locate the dinosaur and teleport it off the island, preventing it's eventual mutation.
The Futurians and Japanese of the 1990s arrive on a Pacific Island named Lagos in 1944. Amid the final stage of Pacific War, a Japanese unit is opposing a US amphibious landing of the island. The time travel group secretly observe the battle. The Japanese unit is almost eliminated by the US landing unit, but the Godzillasaurus, a T-Rex-like ordinary animal, comes out of the jungle and kills the American soldiers. The US ship fires, heavily injures the Godzillasaurus, and then departs. The remaining Japanese unit salutes the injured Godzillasaurus and leaves as well several days later. The Futurians then teleport the Godzillasaurus to the present, then into the Bering Sea, so that it can't be hit by atomic bombs, and return to the future.
Unknown to the Japanese, however, the Futurians have replaced the Godzillasaurus with three genetically engineered creatures called Dorats, who then were exposed to radiation of the nuclear test and mutated into the three-headed, dragon-like King Ghidorah, who appears in present Japan. It is then, that the Futurians' true malevolent intentions are exposed: The story they tell Japanese of 1990s is a lie. The true history of the future is that despite damages by Godzilla, Japan with her giant corporations would grow into a corrupt super power that affects the future world greatly; King Ghidorah is a controlled weapon the Futurians made to damage Japan further, in order to keep her from becoming a super power. However Wilson and Grenchiko are more ambitious. They want to use King Ghidorah to delete Japan from history completely. Emmy disagrees with that. She reprogrammed M11 and leaves the mother ship to tell Terasawa the truth.
Terasawa and others then seek out Godzillasaurus to create a new Godzilla, who is the only force powerful enough to defeat King Ghidorah and the Futurians. They borrow a nuclear submarine from Shindo Heavy Industry, a successful giant corporation established in post War Japan by Shindo, a former officer who was saved by and saluted to the then injured Godzillasaurus on Lagos Island.
Unknown to the Japanese or Futurians, the Godzillasaurus they had transported to the Bering sea had already been mutated. This was because a Soviet nuclear submarine had sunk in the Bering sea during the 1970s. As the Futurians put it, the birth of Godzilla was an unavoidable event, as long as there're nuclear weapons. The Japanese realize this too late, as the sub they sent encounters the already mutated Godzilla. Godzilla attacks the sub and absorbs its power, causing him to become even larger than before.
Wilson and Grenchiko sent King Ghidorah to combat it ashore in Hokkaidō. Ghidorah almost strangles Godzilla to death, but at mean time Emmy, Terasawa and the android sabotage the mother ship. Ghidorah's motion is affected and then it is defeated by Godzilla. Godzilla decapitates its middle head, and has it sink into bottom of the sea. Emmy and others teleport the mother ship in front of Godzilla and leave. Godzilla destroys the ship along with Wilson and Grenchiko on board.
Godzilla then sets out to destroy Japan. Emmy and M11 go back to future with the time traveling shuttle for help. Godzilla enters Tokyo and stands before the headquarters of Shindo Heavy Industry, where Shindo himself stays to wait for Godzilla. Shindo and Godzilla look into each other's eyes for a moment and Godzilla destroys the Shindo headquarter completely. Then Emmy comes back from future with a resurrected King Ghidorah. King Ghidorah is cryogenically preserved in the sea to 2204, when Emmy and the central Futurian government make it a cyborg under Emmy's command: Mecha-King Ghidorah. Emmy uses it to battle Godzilla. In the ensuing fight, Godzilla and Mecha Ghidorah level the center of Tokyo. Emmy uses Mecha Ghidorah's grappling cables to lift Godzilla into the sky. Godzilla continues to fight Ghidorah and sinks them both into the sea. Then Emmy says goodbye to Terasawa, whom she identifies as one of her ancestors, and goes back to future. However, on the bottom of the sea, Godzilla awakens and roars.
- Kenichiro Teresawa: The protagonist of the film; a biographer of Godzilla who aids Emmy, the female lead of this Godzilla film, to stop Futurians.
- Emmy Kano: A Futurian-human who is a descendant of Teresawa 200 years apart, who realizes that her boss is a villain to destroy Japan.
- Chuck Wilson: A villainous Futurian-human who wants to bring advanced technology after controlling Ghidorah to destroy Japan.
- Miki Saegusa: A woman who does not hate Godzilla for unknown reasons, but studies in interest about Biollante from the 1989 film.
- The Prime Minister: Somehow like a normal Japanese man, he realizes the nuclear weapon banning,he had a pretty garden which Ghidorah destroyed.
- M-11: A Futurian-robot, who, first worked with Chuck Wilson, later became a good person, stopping the Futurians from going to their own time.
- Godzilla: A powerful, feared reptile who was born in 1984, and was first considered a threat, later was the only Defender to stop King Ghidorah.
- King Ghidorah: A villain with three-heads forming a dragon that obeys the Futurians to destroy Japan, the film's main antagonist.
- Mecha-King Ghidorah: A robot controlled by Emmy for good reasons to bring Godzilla off rampaging Japan, and stands as the best weapon of mankind.
The film sold approximately 2,700,000 tickets in Japan, and grossed around $11,000,000.
- The big white building in Shinjuku that takes a beating from Mecha-King Ghidorah and Godzilla during the final battle is the main center for tax in Japan, during the cinema showing the audience cheered when it was destroyed.
- The Godzilla suit predominantly used in this film has been nicknamed "Ghidogoji", and was in fact the same "Biogoji" suit used in 1989's Godzilla vs Biollante, although slightly modified.
- Stuntman "Hurricane" Ryu, who portrayed King Ghidorah and Mecha-King Ghidorah, would later return to play Battra in Godzilla vs. Mothra (1992), Baby Godzilla in Godzilla vs Mechagodzilla (1993), and Godzilla Junior in Godzilla vs Destoroyah (1995).
- Many if not all of the explosion sounds in this film are used in many of the incarnations of the Gundam brand of anime as well as some other mecha series.
- A loose-end that deserves mention involves King Ghidorah and Mecha-King Ghidorah. In the beginning of the film, Grenchiko states that a person cannot exist in the same time twice; one of the two would vanish. However, when Godzilla defeats King Ghidorah, the monster falls into the Sea of Okhotsk, where it stays for 200 years. In 2204, Ghidorah is resurrected as a cyborg and returned to 1992. However, as the wounded King Ghidorah is still laying in the sea when Mecha-King Ghidorah arrives, two Ghidorahs clearly exist in the same time. As if to further contradict Omori's law, when Mecha-King Ghidorah is defeated by Godzilla, it to falls into the Sea of Okhotsk, meaning two Ghidorahs not only coexist in the same time, but in the same place as well. This seems to be a clear violation of Grenchiko's statement. However, it is possible that once Mecha-King Ghidorah came to the past, the body of the previous Ghidorah that was lying in the Sea of Okhotsk vanished as Grenchiko said would happen; Mecha-King Ghidorah could then take the previous Ghidorah's place in the sea. The remains of Mecha-King Ghidorah would later be used to create MechaGodzilla 2 in Godzilla vs. MechaGodzilla 2.
- The scene with M-11 chasing Kenichiro and Emmy might be homage to Shinya Tsukamoto's Tetsuo: The Iron Man.