In 1984, the Japanese fishing vessel Yahata Maru is caught in strong currents off the shores of Daikoku Island. As the boat drifts into shore, the island begins to erupt, and a giant monster lifts itself out of the volcano. A few days later, reporter Goro Maki is sailing in the area and finds the vessel intact but deserted. As he explores the vessel, he finds all the crew dead except for Hiroshi Okumura, who has been badly wounded. Suddenly a giant Shockirus sea louse[b] attacks him but he is saved by Okumura.
In Tokyo, Okumura realizes by looking at pictures that the monster he saw was a new Godzilla. Maki writes an article about the account, but the news of Godzilla's return is kept secret and his article is withheld. Maki visits Professor Hayashida, whose parents were lost in the 1954 Godzilla attack.[c] Hayashida describes Godzilla as a living, invincible nuclear weapon able to cause mass destruction. At Hayashida's laboratory, Maki meets Okumura's sister, Naoko, and informs her that her brother is alive and at the police hospital.
A Soviet submarine is destroyed in the Pacific. The Soviets believe the attack was perpetrated by the Americans, and a diplomatic crisis ensues, which threatens to escalate into nuclear war. The Japanese intervene and reveal that Godzilla was behind the attacks. The Japanese cabinet meets to discuss Japan's defense. A new weapon is revealed, the Super X, a specially-armored flying fortress that will defend the capital. The Japanese military is put on alert.
Godzilla attacks the Mihama nuclear power plant in Shizuoka Prefecture. While feeding off the reactor, it is distracted by a flock of birds and leaves the facility. Hayashida believes that Godzilla was distracted instinctively by a homing signal from the birds. Hayashida, together with geologist Minami, propose to the Japanese Cabinet, that Godzilla could be lured back to Mount Mihara on Ōshima Island by a similar signal, and a volcanic eruption could be started, capturing Godzilla.
Prime Minister Mitamura meets with Soviet and American envoys and declares that nuclear weapons will not be used on Godzilla, even if Godzilla were to attack the Japanese mainland. Meanwhile, the Soviets have their own plans to counter the threat posed by Godzilla, and a Soviet control ship disguised as a freighter in Tokyo Harbor prepares to launch a nuclear missile from one of their orbiting satellites should Godzilla attack.
Godzilla is sighted at dawn in Tokyo Bay heading towards Tokyo, causing mass evacuations. The JASDF attacks Godzilla but fails to stop its advance on the city. Godzilla soon emerges and makes short work of the JSDF stationed there. The battle causes damage to the Soviet ship and starts a missile launch countdown. The captain dies as he attempts to stop the missile from launching. Godzilla proceeds towards Shinjuku, wreaking havoc along the way. Godzilla is confronted by four laser-armed trucks and the Super X. Because Godzilla's heart is similar to a nuclear reactor, the cadmium shells that are fired into its mouth by the Super X seal and slow down its heart, knocking Godzilla unconscious.
The countdown ends and the Soviet missile is launched, but it is destroyed by an American counter-missile. Hayashida and Okumura are extracted from Tokyo via helicopter and taken to Mt. Mihara to set up the homing device before the two missiles collide above Tokyo. The destruction of the nuclear missile produces an electrical storm and an EMP, which revives Godzilla once more and temporarily disables the Super X.
An enraged Godzilla bears down on the Super X just as it manages to get airborne again. The Super X's weapons prove ineffective against the kaiju, resulting in even more destruction in the city as Godzilla chases it through several skyscrapers. Godzilla finally destroys the Super X by dropping a skyscraper on top of it. Godzilla continues its rampage until Hayashida uses the homing device to distract it. Godzilla leaves Tokyo and swims across Tokyo Bay, following the homing device to Mount Mihara. There, Godzilla follows the device and falls into the mouth of the volcano. Okumura activates detonators at the volcano, creating a controlled eruption that traps Godzilla inside.
In the aftermath of Godzilla's attack on Tokyo and later imprisonment at Mount Mihara, in 1985, Godzilla's cells are secretly delivered to the Saradia Institute of Technology and Science in Saradia, where they are to be merged with genetically modified plants in the hope of transforming Saradian deserts into fertile land and ending the country's economic dependence on oil wells. Dr. Genshiro Shiragami and his daughter, Erika, are enlisted to aid with the project, but a terrorist bombing destroys the institute's laboratory, ruining the cells and killing Erika.
Five years later, in 1990, Shiragami has returned to Japan and merged some of Erika's cells with those of a rose in an attempt to preserve her soul. Meanwhile, scientist Kazuhito Kirishima and Lieutenant Goro Gondo of the JSDF are using the Godzilla cells they collected to create "Anti-Nuclear Energy Bacteria" (ANEB), hoping it can serve as a weapon against Godzilla should it return. They attempt to recruit Shiragami to aid them, but are rebuffed.
International tensions increase over the Godzilla cells, as they are coveted by both the Saradia Institute of Technology and Science and the American rival Bio-Major organization. An eruption from Mount Mihara causes tremors across the area, including Shiragami's home, badly damaging the roses. Shiragami agrees to join the JSDF's effort and is given access to the Godzilla cells, which he secretly merges with one of the roses. A night later, Bio-Major and Saradian agents break into Shiragami's lab, but are attacked by a large plant-like monster, named "Biollante" by Shiragami, which later escapes to Lake Ashi.
Bio-Major agents plant explosives around Mount Mihara and blackmail the National Diet, warning the explosives will be detonated and thus free Godzilla if the cells are not handed over. Kirishima and Gondo attempt to trade, but Saradian agent SSS9 thwarts the attempt and escapes with the cells. The explosives are detonated, and Godzilla is released. Godzilla attempts to reach the nearest power plant to replenish his supply of nuclear energy, but Biollante calls out to Godzilla.
Godzilla arrives at the lake to engage Biollante in a vicious battle, and emerges as the victor. Godzilla then proceeds toward the power plant at Tsuruga, but psychic Miki Saegusa uses her powers to divert Godzilla toward Osaka instead. The city is quickly evacuated before Godzilla makes landfall. A team led by Gondo meet Godzilla at the central district and fire rockets infused with the ANEB into its body, but Gondo is killed in the process, leaving Godzilla unharmed.
Kirishima recovers the cells and returns them to the JSDF. Shiragami theorizes that if Godzilla's body temperature is increased, the ANEB should work against it. The JSDF erects microwave-emitting plates during an artificial thunderstorm, hitting Godzilla with lightning and heating up its body temperature during a battle near the shores of Wakasa Bay. Godzilla is only moderately affected, but Biollante, having evolved into a more powerful form, arrives to engage Godzilla in battle once again.
After a long battle, Godzilla fires an atomic breath inside Biollante's mouth, mortally wounding Biollante. Godzilla is exhausted by the effects of the ANEB and faints. Biollante escapes by splitting apart into glowing spores, rising into space. As the spores ascend, they form an image of Erika. As Shiragami watches the scene, he is shot by SSS9. Kirishima chases and briefly fights with SSS9, with the agent being killed when Sho Kuroki activates a microwave plate he was standing on. Afterwards, Godzilla reawakens and returns to the ocean to recover.
Two years after his battle with Biollante, Godzilla is still weakened from being infected by the Anti-Nuclear Energy Bacteria (ANEB). Meanwhile, science fiction author Kenichiro Terasawa learns of a group of Japanese soldiers stationed on Lagos Island during the Gilbert and Marshall Islands campaign; where they were threatened by American forces, before being saved by a mysterious dinosaur, Godzillasaurus, which Terasawa theorizes to have mutated into the first Godzilla due to nuclear notes on the island. Powerful businessman and veteran, Yasuaki Shindo, who commanded the Lagos Garrison, confirms Godzillasaurus' existence.
Soon, a UFO named MOTHER lands near Mount Fuji. When the JSDF investigates, MOTHER is revealed to be a time machine piloted by the Futurians — Wilson, Grenchiko, Emmy Kano, and the android M-11 — who explain that they are from the year 2204, claiming Godzilla has completely destroyed Japan. The Futurians plan to travel back to 1944 and remove Godzillasaurus from Lagos Island before the nuclear tests, preventing its mutation into Godzilla. To prove themselves, Emmy presents a copy of Terasawa's book, which he's yet to publish.
The Futurians, Terasawa, Miki Saegusa, and Professor Mazaki, travel back to 1944 to Lagos Island, where Japanese forces led by Shindo fight with attacking American forces. As per Shindo's story, Godzillasaurus fights off the Americans, but is mortally wounded by U.S. Navy. After Shindo and his men leave the island, M-11 has Godzillasaurus teleported from Lagos Island to the Bering Strait. Before departing, the Futurians secretly leave three genetic-engineered dragons called Dorats on Lagos Island, which are later irradiated by nuclear tests, mutating and merging King Ghidorah. Returning to 1992, the Futurians use Ghidorah to subjugate Japan and issue an ultimatum of surrender.
Becoming sympathetic for Japan’s people, Emmy reveals to Terasawa the truth behind the Futurians' mission: in the 23rd century, Japan is an economic superpower surpassing the United States, Russia, and China, even buying out South America and Africa. The Futurians sought to change history and prevent this by creating Ghidorah and having him destroy present-day Japan; and planned to erase Godzilla from history to prevent him from threatening their plans. After M-11 brings Emmy back to MOTHER, she reprograms the android to help her.
Shindo plans to send his nuclear submarine to the Bering Strait and irradiate Godzillasaurus, and recreate Godzilla. However, Terasawa discovers that a Soviet nuclear submarine sank there in the 1970s, releasing enough radiation to mutate Godzillasaurus into the current Godzilla. Godzilla destroys Shindo's submarine and feeds on the radiation, consequently recovering from the ANEB and becoming larger. Godzilla arrives in Japan and faces Ghidorah. M-11 and Terasawa help Emmy sabotage MOTHER's control over Ghidorah, causing Ghidorah to lose focus, before Godzilla blasts off Ghidorah's middle head. After sending Ghidorah crashing into the Sea of Okhotsk, Godzilla destroys MOTHER, killing Wilson and Grenchiko.
Godzilla turns his ire on Japan, rampaging from Sapporo to Tokyo, where he kills Shindo after seemingly recognizing him. Emmy travels to the future with M-11 and returns having created Mecha-King Ghidorah, a cyborg version of Ghidorah. The cyborg is initially ineffective in its battle with Godzilla, but manages to restrain and carry Godzilla out of Japan. Godzilla breaks from his restraints causing both to fall into the ocean, destroying Mecha-King Ghidorah. Emmy returns to the future with M-11, but not before revealing to Terasawa that she is his descendant. Back in the ocean floor, a still living Godzilla regains consciousness over Ghidorah's remains.
Following the battle with Mecha-King Ghidorah in mid-1992,[a] a meteoroid crashes in the Izu–Ogasawara Trench and awakens Godzilla from hibernation.
Six months later, ex-archaeologist Takuya Fujito is detained after stealing an ancient artifact in Thailand. Later, Ryuzo Dobashi, a representative of the Japanese prime minister, offers to drop Takuya's charges in exchange for exploring Infant Island in Indonesia with his ex-wife, Masako Tezuka and Kenji Ando, the secretary of the rapacious Marutomo Company.
After arriving on Infant Island, the trio find a cave containing a depiction of two giant moths in battle. Further exploration leads them to a giant egg and a pair of diminutive humanoids called the Cosmos, who identify the egg as belonging to Mothra. The Cosmos tell of an ancient civilization that tried to control the Earth's climate 12,000 years ago, thus provoking the Earth into creating Battra, a male divine moth with a ferocious appearance that vaguely resembles Mothra. Battra destroyed the civilization and their weather-controlling device but then became uncontrollable, and started to harm the very planet that created him. Mothra was then sent by the Earth to fight Battra, who eventually sealed in the Arctic Ocean by the former.
The Cosmos explain how the meteoroid uncovered Mothra's egg, and may have awoken Battra, who is still embittered over humanity's interference in the Earth's natural orders. The Marutomo Company sends a freighter to Infant Island to pick up the egg, ostensibly to protect it. As they are sailing, Godzilla surfaces and heads toward the newly hatched Mothra larva. Battra soon appears in his larval form and joins the battle, allowing Mothra to retreat. The battle between Godzilla and Battra is eventually taken underwater, where the force of the battle causes a giant crack on the Philippine Sea Plate that swallows the two.
At Manila, Masako and Takuya later discover Ando's true intentions when he takes the Cosmos to Marutomo headquarters, where its president Takeshi Tomokane intends to use them for publicity purposes. Mothra enters Tokyo in an attempt to rescue the Cosmos, but the Japan Self-Defense Forces attack her. The wounded Mothra heads for the National Diet Building and starts constructing a cocoon around herself. Meanwhile, Godzilla surfaces from Mount Fuji, while Battra frees himself from the Earth's crust and continues towards Japan. Both Mothra and Battra metamorphose into their imago forms and converge at Yokohama Cosmo World where they begin to fight once more. Godzilla interrupts the battle and initially attacks Battra. Mothra then briefly incapacitates Godzilla and comes to Battra's aid before returning to battle with Godzilla. Battra then returns the favor coming to Mothra's defense.
Regrouping, Mothra and Battra decide to join forces against Godzilla, determining Godzilla to be the greater threat to the planet. Eventually, the two moths overwhelm and carry Godzilla over the ocean. Godzilla kills Battra by biting his throat and blasting his wound with atomic breath. An exhausted Mothra drops Godzilla and the lifeless Battra into the ocean and seals Battra's resting place below the surface by creating a mystical glyph with scales from her wings.
The next morning, the Cosmos explain that Battra had been waiting many years to destroy an even larger meteoroid that would threaten the Earth in 1999. Mothra had promised she would stop the future collision if Battra were to die, and she and the Cosmos leave Earth as the humans bid farewell.
In the aftermath of Mecha-King Ghidorah's defeat by the hand of Godzilla in 1992, the United Nations establishes the "United Nations Godzilla Countermeasures Center" (UNGCC) to stop Godzilla. Their military branch, G-Force, salvages Ghidorah's remains and reverse engineers them to build two anti-Godzilla weapons: an aerial gunship called Garuda and a mecha modeled after Godzilla called Mechagodzilla.
Two years later and one year after Godzilla battled Mothra and Battra in Yokohama, a Japanese team comes across what they assume is a large Pteranodon egg on Adonoa Island, an uncharted island located in Bering Sea. The egg gives off a telepathic signal that attracts Godzilla and Rodan, an adult Pteranodon irradiated by nuclear waste. Godzilla critically wounds Rodan during the ensuing battle while the research team escapes with the egg. It is taken to a research center in Kyoto, where it imprints on young female scientist Azusa Gojo.
Eventually, a juvenile Godzillasaurus hatches from the egg. The creature, named Baby Godzilla by Gojo, is concluded to have been left in the Pteranodon nest with Rodan in a manner similar to the brood parasitism displayed by European cuckoos. Godzilla appears, once again responding to Baby's psychic call. The JSDF mobilizes Mechagodzilla, which intercepts Godzilla as he is heading to Kyoto. The two battle, with Mechagodzilla initially having the upper hand until Godzilla disables the mecha with his energy pulse. Godzilla continues searching for Baby, but the scientists, having discovered the telepathic link between the monsters, shield him from Godzilla. Frustrated, Godzilla destroys most of Kyoto before returning to the ocean.
Tests on the baby reveal that he has a second brain in his hips that controls the animal's movement. The UNGCC assumes that this also holds true for Godzilla's species and decide to use Baby to bait Godzilla into another fight with Mechagodzilla. The "G-Crusher" is installed into Mechagodzilla, which will allow the mecha to penetrate Godzilla's hide and destroy his second brain. Miki Saegusa is ordered to become a part of Mechagodzilla's crew to locate Godzilla's second brain. While she is reluctant due to her mental connection with Godzilla, she agrees. The plan backfires when Rodan, having transformed into Fire Rodan since his battle with Godzilla, responds to Baby's call and intercepts the UNGCC transport.
In response, they send Mechagodzilla and the upgraded Garuda, piloted by Kazuma Aoki, after Rodan instead, which injure him in the process. Godzilla arrives soon after and attacks Mechagodzilla. The fight is evenly matched until Mechagodzilla merges with Garuda to become Super-Mechagodzilla. Mechagodzilla paralyzes Godzilla, but Rodan responds to Baby's call, sacrifices himself, and transfers his power to regenerate Godzilla's second brain. This empowers Godzilla, allowing him to destroy Mechagodzilla.
Godzilla locates Baby, who is initially afraid of Godzilla's gigantic size, but is telepathically convinced by Miki to go with Godzilla, and the two monsters return to the ocean together.
Godzilla's cells brought into space by Biollante in 1990, and Mothra in 1993, are exposed to intense radiation from a black hole, resulting in the birth of an extraterrestrial creature, which quickly makes its way to Earth, destroying a NASA space station along the way.
Meanwhile, members of the United Nations Godzilla Countermeasures Center (UNGCC), Koji Shinjo and Kiyoshi Sato, arrive at Baas Island, the home of Godzilla and his son Little Godzilla, in order to plant a mind control device on Godzilla. The Cosmos, Mothra's twin priestesses, telepathically visit Miki Saegusa and warn her of the extraterrestrial's arrival. M.O.G.U.E.R.A. (Mobile Operations G-Force Universal Expert Robot: Aero-type), a mecha built by the JSDF to replace Mechagodzilla, is sent in to intercept the creature, but suffers damage in the process.
The creature lands on Baas Island and attacks Little. Godzilla intervenes but finds himself overwhelmed, and is powerless to stop the creature from trapping Little in a crystal prison. The creature, dubbed "SpaceGodzilla" by UNGCC, leaves for Japan, with Godzilla in pursuit.
Shortly thereafter, the yakuza, led by McKay, abduct Miki and bring her back to their base in Fukuoka in an attempt to use her psychic abilities to gain control over Godzilla. Miki is rescued by Shinjo, Sato and Yuki before SpaceGodzilla arrives. SpaceGodzilla lands in central Fukuoka and forms a massive fortress of celestial crystals. M.O.G.U.E.R.A., now piloted by Shinjo, Sato and Yuki, arrives to once again battle SpaceGodzilla, but is still no match for it. Godzilla arrives in Kagoshima Bay and battles SpaceGodzilla, but SpaceGodzilla easily gains the upper hand.
The JSDF discovers that SpaceGodzilla is using Fukuoka Tower as a power converter, using it to transform the Earth's core into an energy that SpaceGodzilla can absorb, slowly killing the planet. While Godzilla battles SpaceGodzilla, M.O.G.U.E.R.A. splits into two different mechas: the Star Falcon, a flying battleship piloted by Yuki, and the Land M.O.G.U.E.R.A., a tank with a large drill in front of it piloted by Shinjo and Sato. Both mechas damage the crystal fortress while Godzilla pushes over Fukuoka Tower, cutting off SpaceGodzilla's energy supply. M.O.G.U.E.R.A. quickly reforms and blasts off SpaceGodzilla's crystal-like shoulder formations, weakening it. SpaceGodzilla then critically damages M.O.G.U.E.R.A. but is subsequently incinerated and destroyed by Godzilla's supercharged atomic breath. After SpaceGodzilla's destruction, the JSDF claims that if humanity continues to pollute space, another SpaceGodzilla may appear someday.
As Godzilla makes his way back to Baas Island, Miki uses her psychic powers to remove the mind control device from Godzilla's neck. Meanwhile at Baas Island, Little is freed from the crystal prison and begins blowing atomic bubbles.
One year after the defeat of SpaceGodzilla by the hands of Godzilla and JSDF's mecha M.O.G.U.E.R.A.,[b] Miki Saegusa of the United Nations Godzilla Countermeasures Center (UNGCC) travels to Baas Island to monitor Godzilla and his son Little, only to find the entire island destroyed and both monsters missing as the island was engulfed in an explosion of nuclear fission. Godzilla, now covered in lava-like rashes, subsequently appears in Hong Kong, destroying great swathes of the city with an empowered atomic breath. The JSDF hires college student Kenkichi Yamane, a grandson of Dr. Kyohei who had encountered the first Godzilla,[c] to unravel the mystery of Godzilla's condition. Yamane suspects that Godzilla's heart, which acts as a nuclear reactor, is undergoing a nuclear meltdown as a result of the monster absorbing the energy released from a volcanically triggered uranium deposit on Baas Island. Yamane theorizes that when Godzilla's temperature reaches 1,200 °C (2,190 °F), it will lead to a thermonuclear explosion with enough energy to melt the Earth down to its core.
The JSDF deploys the Super X III, an aerial combat vehicle outfitted with ultra-low temperature lasers, in an attempt to reverse Godzilla's self-destruction. While Godzilla's meltdown is not stopped, it is halted long enough to render Godzilla temporarily unconscious. Meanwhile, a colony of Precambrian organisms mutated by the Oxygen Destroyer used to defeat the first Godzilla are awoken during the construction of the Tokyo Bay Aqua Line. The organisms combine into several human-sized crustacean monsters and engage the JSDF in several deadly skirmishes. The monsters, dubbed "Destoroyah", are revealed to be vulnerable to subzero temperatures and are temporarily held at bay with low-temperature lasers. The Destoroyah respond to the threat by merging into a larger creature, which destroys the lasers and takes to the skies in its flying form.
Godzilla awakens, his condition having deteriorated to the point that his meltdown could potentially destroy the Earth through a China syndrome-like incident. Miki locates the now grown-up Little, redubbed "Godzilla Junior", and telepathically lures him to Tokyo, hoping that Godzilla will follow and be killed by Destoroyah. Junior arrives and battles Destoroyah, who absorbs Junior's DNA before being seemingly defeated. Godzilla arrives at Haneda Airport and reunites with Junior. Destoroyah, bolstered by Junior's DNA, drops Junior onto the Ariake Coliseum and blasts a Micro-Oxygen beam into Junior, fatally wounding him.
After driving off Destoroyah and unsuccessfully attempting to revive Junior, Godzilla's bereavement accelerates the rate of his meltdown. In the ensuing battle with Destoroyah, Godzilla's temperature reaches a critical state, allowing him to wound Destoroyah. As the injured Destoroyah tries to retreat, the JSDF fires their low-temperature lasers at its wings, causing it to plummet to its death onto the superheated ground.
As Godzilla goes into meltdown, the JSDF is able to minimize the damage with its low-temperature weapons. While successful in preventing Earth's destruction, Godzilla slowly dies from his meltdown, which renders Tokyo uninhabitable. The radiation in Tokyo abruptly decreases to background levels, as Junior's lifeless body had absorbed Godzilla's radiation, resurrecting and transforming him into the new Godzilla.