The giant monster dubbed "Godzilla" is regarded as a literal force of nature in Japan. The Godzilla Prediction Network (GPN) functions independently to study the monster and predict its landfalls. Meanwhile, the scientists of Crisis Control Intelligence (CCI) find a sixty-million-year-old unidentified flying object (UFO) deep in the Japan Trench. As CCI attempts to raise the UFO to study it, it takes off into the sky on its own. Godzilla arrives in a village and then battles the Japan Self Defense Forces, now equipped with powerful Full Metal Missiles, until the UFO appears, searching for genetic information that only Godzilla possesses. It fights Godzilla, driving the monster underwater, and then lands to replenish its solar power.
Yuji Shinoda, the founder of the GPN, discovers the secret to Godzilla's regenerative properties (named Organizer G1 in the Japanese version, but Regenerator G1 in the North American release), but so has the UFO. It frees itself from the JSDF's attempts to contain it, and heads for Shinjuku. After landing atop Tokyo Opera City Tower, it begins to drain all the files about Godzilla from Tokyo's master computers. As it begins to alter the oxygen content of the surrounding atmosphere, CCI attempts to destroy the UFO using explosive charges, but Shinoda, attempting to find out more about the aliens, is nearly caught in the blast. He survives, and joins his peers on a nearby rooftop, watching the UFO. Almost in response, the UFO broadcasts its message of invasion and creating a new "thousand-year kingdom" on Earth, and Shinoda reveals that the aliens are after the regenerative properties contained inside Godzilla's DNA so that they may use it to re-form their bodies.
Godzilla arrives and again battles the UFO. However, he is subdued by the UFO's assault, and the UFO absorbs some of Godzilla's DNA, which the aliens use to reform themselves outside the spaceship as the gigantic Millennian. However, the Millennian is unable to control Godzilla's genetic information in the DNA and mutates into a deformed monster named Orga. Godzilla recovers and brings down the UFO before fighting Orga, but Orga, having absorbed the regenerative properties of Godzilla's DNA, is highly resistant to injury. Orga retaliates and extracts more of Godzilla's DNA to become a perfect clone. Godzilla breaks free and sets Orga ablaze with his atomic breath attack, but Orga re-emerges and attempts to swallow Godzilla whole. As Orga begins to transform, Godzilla charges a nuclear pulse and unleashes it, vaporizing Orga's entire upper body and killing it. Mitsuo Katagiri, head of CCI, dies when Godzilla partially destroys the roof of the building where he, Shinoda, and the authorities were observing the battle. Those remaining on the roof reminisce on how Godzilla was wrought by human ambition, prompting Shinoda to suggest that "Godzilla exists in us", as Godzilla begins rampaging through Tokyo.
In 1954, repeated nuclear testing revives the creature called Godzilla, who proceeds to decimate Tokyo in retaliation.[a] Afterwards, the capital of Japan is moved from Tokyo to Osaka during Tokyo's reconstruction. In 1966, Japan abandons the use of nuclear power after Godzilla attacks Tōkai Nuclear Power Plant to feed on its energy. In 1996, Japan develops a new form of "clean" plasma energy to replace nuclear energy, but Godzilla returns once more and attacks a plasma energy reactor in Osaka. As a result, plasma energy is also banned due to fears that it will continue to attract Godzilla, while the Japanese government establishes a special unit of the Japan Self-Defense Forces, known as the "G-Graspers", dedicated to combating Godzilla if he returns again.
In 2001, the G-Graspers, led by Major Kiriko Tsujimori and assisted by rebellious scientist Hajime Kudo, have developed an experimental satellite-based weapon that fires miniature black holes, codenamed Dimension Tide, in hopes of killing Godzilla. A test firing of the weapon temporarily opens a wormhole, through which a giant prehistoric dragonfly known as a Meganula briefly enters the present time and deposits an egg sac, before returning through the wormhole. A boy named Jun Hayasaka finds the Meganula's egg sac, and takes it with him when he moves to Tokyo. When the egg sac starts oozing a strange liquid, Jun dumps it in the sewer, where the egg sac splits into a mass of eggs and hatches into giant dragonfly nymphs called Meganulon. At night, a Meganulon kills a couple and molts into a new Meganula. Many more soon emerge, while their underground activity causes flooding across large areas of Tokyo.
Meanwhile, Godzilla appears again in the ocean near Japan, despite the country's bans on both nuclear and plasma energy. While Godzilla battles the G-Graspers, who manage to lure him ashore on Kikaijima Island using their advanced Griffon aircraft so Dimension Tide can target him, the swarm of Meganulon have all metamorphosed into their Meganula forms, and are attracted to Godzilla's energy. The swarm arrive on the island and attack Godzilla, but he manages to kill most of them. During the battle, the Dimension Tide is fired, but the strike misses and Godzilla survives. The surviving Meganula fly back to the flooded Shibuya, with Godzilla seemingly following them. With the last of their strength, the Meganula inject some of Godzilla's energy into the nymph form of their massive queen, Megaguirus, allowing her to molt into her adult form. After destroying part of Shibuya, Megaguirus flies to Odaiba and faces Godzilla. The two monsters engage in a lengthy battle, but Godzilla ultimately kills Megaguirus by breaking her stinger and then blasting her with his atomic breath.
It is revealed that Godzilla has been attracted to a secret plasma energy project housed at Tokyo's Science Institute, in violation of the ban. As the Dimension Tide satellite begins falling out of orbit, Tsujimori pilots the Griffon directly above Godzilla, allowing the Dimension Tide to lock on to her craft and fire just before burning up on reentry. Tsujimori ejects before the Griffon crashes into Godzilla, who fires his atomic breath at the descending black hole, but seemingly vanishes.
Later, Tsujimori again enlists Kudo to investigate unusual seismic activity, suspecting that Godzilla might have survived. In a post-credits scene, Jun hears Godzilla's roar as an earthquake strikes Tokyo.
During a briefing with the Japan Self-Defense Forces (JSDF) regarding the first Godzilla's attack and death,[b] admiral Taizo Tachibana is alerted about an American nuclear submarine that went missing off Guam. Search and rescue units find the submarine destroyed and capture footage of the creature's dorsal plates nearby.
Tachibana's daughter and reporter, Yuri, films a docudrama with her production crew at Mount Myōkō, where a mysterious earthquake briefly occurs. It occurs again later that night, burying a biker gang and leaving a surviving trucker, who witnesses the subterranean monster Baragon. The next day, Yuri's colleague Teruaki Takeda supports her theory that a monster may have caused the mysterious earthquakes and gives her a book called The Guardian Monsters.
At Lake Ikeda, Mothra in her larval form attacks a group of teenage vandals who disturbed her shrine and builds her cocoon. Yuri interviews Hirotoshi Isayama, an mysterious old man who explains the legend of the guardian monsters, iterating that they must be awakened before Godzilla, an undead creature, destroys Japan. Yuri and her colleagues visit the guardian monsters' shrine, where she finds a stone before returning to continue interviewing Isayama. In the process, she discovers that the souls of soldiers and civilians who were killed during the Pacific War are embedded within Godzilla and are lashing out due to modern Japan's denial of its past crimes. Meanwhile in Aokigahara, a suicidal man accidentally encounters a frozen 1,000-year-old ancient dragon called King Ghidorah.
Godzilla and Baragon surface and battle in Hakone, with the former killing the latter. Yuri is injured during the fray and goes on her own after Takeda refuses to take her to Godzilla's location. After the jets fail to stop Godzilla, Tachibana sets up a defense line in Yokohama. Mothra metamorphoses into her imago form and joins Ghidorah in battling Godzilla, but are overpowered. Godzilla attempts to attack the soldiers, but Mothra sacrifices herself and imbues her spirit into Ghidorah. An empowered Ghidorah injures and drags Godzilla underwater. Amidst this, Tachibana and his colleague Yutaka Hirose board miniature submarines to launch D-3 missiles into Godzilla's wound.
During Yuri and Takeda report on the struggle from Yokohama Bay Bridge that later collapses from Godzilla's atomic breath, the shrine stone falls from Takeda's pocket and revives Ghidorah, who saves Yuri and Takeda from their fall before they swim ashore while the monsters continue to fight. Godzilla kills Ghidorah, which unleash the spirits of the guardian monsters to drag Godzilla underwater, allowing Tachibana enters Godzilla's body through its mouth. As Godzilla attempts to kill Yuri and Takeda, Tachibana fires a D-3 missile at its wound, causing its atomic breath to escape through the gaping wound and build pressure within Godzilla. Tachibana escapes as Godzilla sinks and explodes after attempting to kill the former with its atomic breath.
As Japan rejoices at their victory, Yuri's colleagues discover all trace of Isayama has vanished from their recordings and that he was killed during the first Godzilla attack. Meanwhile, Yuri reunites with Tachibana, who salutes his colleagues and the guardian monsters. On the ocean floor, Godzilla's disembodied heart continues to beat.
Forty-five years after the first Godzilla's attack and death, maser-cannon technician lieutenant Akane Yashiro of Anti-Megalosaurus Force (AMF) is unable to kill a new member of Godzilla's species during her first fight with him at Tateyama. During the battle, she panics and accidentally knocks a jeep off the road, where Godzilla steps on it, killing her comrades inside.
As a result, Akane is demoted while scientists, including single father Tokumitsu Yuhara, are gathered to build a cyborg mecha from the first Godzilla's skeleton. In time, the "MFS-3 Kiryu" is finished and inducted into the Japan Xenomorph Self-Defense Forces (JXSDF) along with its human pilots, the Kiryu Squadron, with Akane as the primary pilot. However, memories of her actions during the first battle still linger as one of her squadron mates, 2nd lieutenant Susumu Hayama, hates her because his brother was among those killed.
Four years later, Kiryu is unveiled in a global presentation where its remote systems, use of command aircraft, and Absolute Zero Cannon are shown. Simultaneously, Godzilla returns and Kiryu is launched into battle. In the midst of this, however, Godzilla's roar causes Kiryu to experience memories of its past life and go berserk while Godzilla retreats. The horrified Kiryu Squadron is powerless to stop the rampaging Kiryu until it runs out of energy and is brought back to headquarters for repairs.
Meanwhile, Akane deals with Hayama's attempts to make her leave and Yuhara's attempts to get to know her despite her desiring solitude, though she begins to develop a bond with Yuhara's young daughter Sara. As Godzilla mounts another attack, the repaired Kiryu is deployed and confronts Godzilla once more. Kiryu gains the upper hand, but as it prepares the Absolute Zero Cannon, Godzilla knocks Kiryu away with his atomic breath and diverts the blast. With Kiryu disabled and the remote piloting system offline, Akane orders Hayama to land his command craft so that she can use Kiryu's internal backup cockpit. Before she leaves, Hayama wishes her luck, forgiving her.
Piloting Kiryu directly, Akane closes in on Godzilla, hoping to use the Absolute Zero Cannon at point-blank range. As the two monsters collide, Akane uses Kiryu's thrusters to propel them out to the ocean before firing. In the aftermath, an injured Godzilla retreats while Kiryu is heavily damaged. With Kiryu successful in repelling Godzilla, it is taken back to base for repairs.
In a post-credits scene, Akane agrees to have dinner with the Yuharas and salutes Kiryu.
The Shobijin visit Shinichi Chujo, his scientist nephew Yoshito, and his grandson Shun to warn them that Godzilla continues returning to Japan because the Japanese government used the first Godzilla's skeleton in the cyborg MFS-3 Kiryu's construction. If the government returns the skeleton to the ocean, Mothra, the descendant of the first Mothra who attacked Japan forty-three years ago, will take Kiryu's place in defending Japan.
As Kiryu undergoes repair and modifications, the Kiryu squadron is sent to the United States for further training, with Kyosuke Akiba taking Akane Yashiro's place should Godzilla return while she is away. Due to the first Mothra's attack, Japanese prime minister Hayato Igarashi denies Chujo's request, but agrees to discontinue the Kiryu project once the cyborg exterminates Godzilla. Sometime later, Godzilla resurfaces to attack Tokyo despite his injuries sustained since the last battle with Kiryu. Chujo and Shun summon Mothra to battle Godzilla. With the repairs finished, the government deploys Kiryu, but Godzilla knocks both it and Mothra out, injuring Chujo and Shun during the fray.
Meanwhile on Himago Island, the uncharted volcanic island in Ogasawara island chain, twin Mothra larvae hatch from their egg and rush to help their mother. As Yoshito, with help from the Shobijin, uses a maintenance hatch to enter and repair Kiryu from its internal backup cockpit, the Japan Xenomorph Self-Defense Forces (JXSDF) and larvae try to hold Godzilla off, but Mothra sacrifices herself to protect the latter from Godzilla's atomic breath while a separate attack warps Kiryu's maintenance hatch, trapping Yoshito inside. Nonetheless, he completes the repairs, allowing Kiryu to wound Godzilla before its spirit is reawakened by Godzilla's roar.
After the larvae bind Godzilla in a silk cocoon, Akiba is ordered to kill Godzilla per Yoshito and the Shobijin's request. However, Kiryu lifts Godzilla and uses its boosters to carry them both out to sea. Akiba's fellow pilot, Azusa Kisaragi, blasts the hatch open. Kiryu turns over to let Yoshito escape before it plunges into the ocean and drifts into an underwater trench with Godzilla. As Japan celebrates their victory, Yoshito bids Kiryu farewell while the larvae return to Infant Island with the Shobijin.
In a post-credits scene, an undisclosed laboratory is shown with canisters containing the DNA of numerous monsters.
Over the course of the 20th century, environmental disasters cause the appearance of giant monsters and superhumans, dubbed "mutants", who are then recruited into the Earth Defense Force (EDF) to battle the monsters. The strongest of these monsters is Godzilla, who becomes the EDF's greatest enemy and frequently threatens mankind over the years. In Antarctica, Godzilla is finally imprisoned under the ice during a battle with the powerful EDF warship Gotengo.
Many years later, in 2004, an upgraded Gotengo, now commanded by Captain Douglas Gordon, battles and destroys Manda in the English Channel off the coast of Normandy, but the ship sustains serious damage during the battle and Gordon is suspended from the EDF. Mutant EDF ensign Shinichi Ozaki is tasked with guarding a U.N. biologist, Dr. Miyuki Otonashi, who is sent to study a mummified monster. As they examine it, they are briefly teleported to Infant Island by the Shobijin, who reveal the mummified monster as Gigan, an extraterrestrial cyborg that attempted to destroy the Earth ten thousand years earlier, and was ultimately subdued by Mothra. They warn that a battle between good and evil will happen soon, and that Ozaki must choose a side.
Several giant monsters attack major cities around the world: Rodan attacks New York City, Zilla attacks Sydney, Anguirus attacks Shanghai, King Caesar attacks Okinawa, Kamacuras attacks Paris, Kumonga attacks Monument Valley in Arizona, and Ebirah attacks Tokai. Meanwhile, Minilla, Godzilla's son, is found in Aokigahara by Kenta Taguchi and his grandfather, Samon. The EDF engages the monsters until they mysteriously vanish, as a huge alien vessel appears over Tokyo. The aliens introduce themselves as the Xiliens, claim that they eliminated the monsters as a gesture of goodwill, and warn Earth's leaders that an incoming runaway white dwarf star called Gorath will soon impact the Earth, offering their help to destroy it.
After a peace pact is signed between humanity and the Xiliens, Ozaki, Miyuki, and Miyuki's sister Anna, a news reporter, discover that the Gorath shown by the Xiliens is a hologram and that the Xiliens have replaced several members of the EDF and U.N. secretary-general Naotaro Daigo with imposters. After the Xiliens are exposed with help from Gordon and the other mutants, the Xiliens' second-in-command, the Controller, kills his leader to assume command, revealing their plan to use humans as a food source while taking control of all the mutants, except for Ozaki, through a property in their DNA known as "M-base". The Controller also has the monsters under his control through M-base in their DNA, and awakens Gigan to wipe out the EDF. The group escapes in a repaired Gotengo, although Gigan pursues them.
Gordon convinces the Gotengo's crew to travel to Antarctica to release Godzilla, who is immune to the Xiliens' control thanks to his lack of M-base and easily defeats Gigan. The Gotengo then guides Godzilla into a series of battles with the other monsters: he defeats Zilla in Sydney, Kumonga in New Guinea, and Kamacuras in Manazuru. At Hakone, Samon, who witnesses Godzilla’s arrival with Kenta and Minilla, remarks that long ago, humanity’s actions angered Godzilla, leading to his decades of aggression. After Godzilla battles and subdues Rodan, Anguirus and Caesar at Mount Fuji, the Gotengo leads him to Tokyo to defeat the Xiliens.
Ozaki’s comrade Katsunori Kazama sacrifices himself to disable the Xilien mothership’s barrier shield, allowing the Gotengo's crew to penetrate the ship, but they are captured and brought before the Controller as he summons Gorath to Earth. After defeating Ebirah and Hedorah in Tokyo, Godzilla destroys Gorath just before it can hit the Earth, but this unleashes the Xiliens' ultimate weapon, Monster X, and the two monsters battle. A repaired and upgraded Gigan joins Monster X, but is intercepted by Mothra, who manages to destroy him once and for all.
Aboard the Xilien mothership, the Controller reveals that both he and Ozaki are superior beings known as "Keizers", powerful beings distinct from regular mutants born on rare occasions when human DNA and M-base are combined, before directly taking control of Ozaki to turn him against the group. As a fight breaks out, the Controller loses control of Ozaki due to the Shobijins' blessing. Ozaki unlocks his true power and defeats the Controller, who triggers the mothership's self-destruct as the group falls back to the Gotengo moments before the mothership explodes. Godzilla and Monster X continue their battle, but Monster X transforms into its true form, Keizer Ghidorah. Godzilla is overpowered by Keizer Ghidorah, but Ozaki transfers some of his own Keizer energy to Godzilla, giving him the strength to destroy Keizer Ghidorah.
Despite the Gotengo's crew proving instrumental in his victory, an enraged Godzilla shoots down the Gotengo before attempting to attack the vessel's crew. Fortunately, Minilla arrives with Kenta and Samon, and convinces Godzilla to spare the crew. Ozaki, Miyuki, Gordon, Anna, and the other humans watch as Godzilla and Minilla return to the ocean.