At a training lecture for officers of the JSDF, Lt. General Tachibana discusses the history of the JSDF and Godzilla's attack in 1954. Since then, strange creatures have appeared elsewhere in the world, which means Japan must be ever prepared. Monsters have appeared in the United States, even identified as Godzilla, though Japanese scientists dispute the claim. Orders suddenly arrive for General Tachibana and he dismisses the class. Media reports talk of a US Navy nuclear submarine lost in the South Pacific. The Japanese help look for the lost sub with their submersible research ship Satsuma.
The Satsuma prowls the ocean depths. The sub wreck is found, the hull ruptured, possibly from an explosion. A disturbance on the ocean floor rocks the Satsuma and her sister ship. It is some immense monster moving nearby. Only a quick glimpse can be made out, a glimpse of glowing dorsal plates. The monster is Godzilla.
A news crew reports on a legendary monster at Ryokoh Mountain. The reporter is Yuri Tachibana, daughter of the general. The local village chief arrives, protesting the program, complaining that he thought it was a serious documentary, not a horror show. He tells them to leave, wishing to preserve the village's wholesome reputation. Yuri intervenes, mentioning that everyone loves a mystery, quoting an American film about a legendary witch which became a big hit. Afterwards, the town it was set in became a popular tourist site.
A sudden earth tremor rocks the area. After they recover from the earthquake, the village chief agrees enthusiastically that Yuri can publicize the monster legend - and the village. Yuri sees a strange figure, an elderly man, watching her from the woods. But when she glances away, he mysteriously disappears.
That night, the village chief discusses the news report and its implications for the village with a lady friend in a parked car. They are interrupted when a gang of motorcycle riding youths terrorizes them, driving around the car and beating on it. As a parting gesture, one of the bikers decapitates an ancient stone statue nearby. The bikers speed off down the highway, speeding ahead of a truck, narrowly avoiding causing an accident. The gang rides into a tunnel, which crumbles around them, burying them as it collapses. The truck stops at the mouth of the tunnel. The trucker is horrified to see the fanged head of an enormous beast appear before debris blocks the tunnel completely.
Back at Digital BS, a sensationalist trash journalism network, Yuri tells her editor about the earthquake, whose epicenter has moved to cause the tunnel cave-in as well. She wants to investigate it, but Haruki is less enthused, explaining that they have a tight budget and that nobody wants to watch their shows anyway. He says that they don't need truth in their reporting.
At Ryokoh Mountain, the JSDF arrives to try blasting their way into the mountain to reach the people inside. They will use a new boring missile to try and penetrate the mountain. A JSDF officer interviews the shaken truck driver. The man mutters that what he saw was Godzilla.
Yuri and her cameraman Maruo are having dinner and drinks in a restaurant, Yuri complaining about her lack of power and prestige at Digital BS. The science-fiction writer Mitsuaki Takeda joins them, giving Yuri a book, The Legend of the God-Monsters. He says that the source of their mysterious moving earthquake can be found in the book. It will make a good plot for a show.
A mob of rowdy college students vandalizes and loots a closed store on the shore of Lake Ikeda. The drunken youths decide to dispose of the only witness to their crimes, a yapping dog. Two boys uproot a small but heavy stone statue, carrying it back to their comrades, unaware that they are observed by an aged and mysterious figure. The youths put the statue and the dog into a wooden box, close it, and a few of them row out onto the lake. Before they can drown the dog, however, a disturbance in the lake upsets the boat, capsizing it. The students swim to the surface, but something drags them back down one by one. Those still on shore run for their lives as a huge caterpillar creature emerges from the water.
Takeda drives a drunken Yuri home, shocked when he is met by her father. Tachibana takes charge of his daughter, thanking Takeda. In the morning, he asks Yuri how her job is going and if Takeda is her boyfriend. Yuri turns on the TV, learning about the events at Lake Ikeda. She is startled by the news, realising that it is related to the Mount Ryokoh events and that they cannot be a coincidence.
Yuri, Takeda and Maruo head for Mt. Fuji by way of train. Yuri explains that everything is happening just like in the book. Maruo asks if Yuri is still angry about the other night. Takeda relates his unexpected and unsettling encounter with General Tachibana when he took Yuri home.
At a meeting of JSDF commanders, the footage taken by the Satsuma is reviewed. The sub commander, Captain Kiyose, is debriefed by General Tachibana. He says that he believes the object in the footage is Godzilla. The possibility is treated with a certain amount of derision, though a few, like General Tachibana, treat it with the utmost severity.
Yuri and her companions go to the Hongo police station in the Yamanashi Prefecture, near Mt. Fuji. The police chief takes them to the holding cell where they are keeping a crazy old hermit who has been living in the woods, telling people that Godzilla is coming. Yuri is shocked to discover that it is the same old man she saw at Ryokoh Mountain, something that seems impossible given the distances involved. Yuri speaks with the old man, who tells her there is not much time left, she must go to where Ghidorah is sleeping, for without him they are too weak to stand against Godzilla.
The reporters go to a shrine in Fuji Forest. The Legend of the God-Monsters says that there were beasts such as Baragon, Mothra and Ghidorah who were slain by the ancients, their bodies buried under shrines. They were to sleep for ten thousand years in order to honour their souls. It was a practice of making dead foes into gods that was passed on to the Yamato Court. Yuri realises that Ghidorah was buried beneath their very feet. It has been only two thousand years since the time of the legends, so Takeda believes that Ghidorah would not yet be fully grown, if he was he would be the strongest in the world. Yuri finds a statue shard she feels the old man left for her to find. Maruo makes another alarming discovery - since arriving and filming, one of the massive stone plinths near the shrine has disappeared.
Magonoteh Island in the Ogasawara Archipelago. A group of students renting a house relax while a typhoon brews outside. One notices some old pictures and his friend tells him that their landlady said the island where Godzilla first appeared was nearby. This starts some joking about feeling sorry for Godzilla and that he had to be destroyed by the JSDF. The joking stops when a series of tremors rocks the house. An older islander looks out his own front door to see the source of the disturbance. Before he can scream the name of what he sees, Godzilla's foot smashes man and dwelling into ruin.
Yuri reviews her taped interview with the old man, who tells her that Godzilla is more than a simple animal, more than a mutant. If he was only that, bombs and bullets would harm him. He says Godzilla is an aggregate of hateful feelings toward Japan caused by WWII. He is possessed by the spirits of the thousands who died in the Pacific War. Haruki interrupts, asking Yuri if she believes the old man's story. She replies that she doesn't think that he is deluded. He is Professor Isayama, who wrote The Legend of the God-Monsters. Haruki tries to lighten the dour pall cast by the old man's words, mentioning that some relatives of his wife were killed by Godzilla. He doesn't believe Godzilla is relevant to modern times, but says Yuri may continue reporting.
On the tape, Yuri asks Isayama why Godzilla is attacking Japan. He replies that it is because people are forgetting everything. Godzilla is the resentment of all those who died in the war and are being forgotten.
The JSDF main control room. A helicopter searches the devastated Magonoteh Island. As they search, the radio operator receives a report from the helicopter. They are alarmed when a mountain moves. The last sound to come over the radio is Godzilla's shriek, then all is static.
Yuri reads a book about Hopi Indian lore, puzzling over a passage about the earth and rocks remembering and having much to say if only they are asked. Takeda explains that rocks can hold electricity, volcanic rock shows traces of an electric current when under great pressure. Yuri observes that if spirits are made of electricity, then they may be able to be stored in stones. They realise that Isayama may have been trying to release the spirits within the statues in order to support the Yamato monsters. Obviously he wanted to do such a thing to protect Yamato from Godzilla.
In Fuji Forest, a despondent man topples the statue from which the shard Yuri found was chipped. He climbs it, using it as a step while he tries to hang himself. The ground gives way beneath his feet and he falls into an ice cave. The suicide is horrified to see a huge golden monster entombed in the ice, fleeing as he observes each of its three heads.
At a press meeting, the Prime Minister announces that what attacked the US submarine and Magonoteh Island was Godzilla. The waters around Japan have been placed under alert and a search is being conducted. Yuri is angry at her father for not sharing the information, but he says that she must do her own work if she is to be proud of the result. Yuri says she has important information to share with her father.
The Japanese maritime Defense Force searches the waters about Ogasawara for Godzilla, but turn up no trace of the beast.
Yuri visits her father at the Ministry of Defense, showing him the Legend of the God-Monsters. Tachibana is amazed that the places of the accidents correspond so precisely to the origins of the monsters. Takeda explains that the monsters are protectors of Yamato, the country, meaning the land itself, not necessarily the people. Yuri believes the legend is true. Tachibana is disturbed that soldiers who died in the war could be attacking Japan through Godzilla. Yuri explains that she thinks the spirits in Godzilla are other victims of the war - civilians killed in Southeast Asia, American soldiers and Japanese victims of the Atomic Bomb. Captain Kiyose enters and reports to Tachibana, Tachibana informs him that the search for Godzilla has been called off. They are still on a state of alert, but the government will review the Godzilla theory.
Tachibana worries that people have forgotten Godzilla in this peaceful time. He relates that he was there, in 1954, among the fleeing masses when Godzilla attacked Tokyo. He was separated from his parents, and never saw them again. He has never forgotten the cries and screams of the people killed by Godzilla that day.
The Nagano Weather Bureau and JSDF monitor the strange moving earthquake as it rumbles across Japan.
Over lunch, Yuri mentions to Takeda her intention to use her father's story for a future show. Takeda scolds her, saying that he was quite moved by the general's story. If she does such an exploitative thing, no one will find her credible when she tries to tell them about the Yamato monsters. Yuri replies that Takeda doesn't understand journalism. A report on TV about the moving earthquake interrupts them. They realise that its cause must be the monster Baragon.
Lt. General Tachibana discusses the god-monsters with fellow officers. It is pointed out that it could be Godzilla burrowing underground, or an entirely different monster. Tachibana still can't believe how the locations exactly correspond to those in the book.
In the Hongo Police Station, the would-be suicide reports the ice cave and the monster to the police chief. Suddenly, an earthquake rocks the building. Baragon erupts from the ground outside. He knocks down one wall of the police station, exposing the cells and freeing Professor Isayama.
At the Ministry of Defense, Baragon's appearance is reported, identified as being the same species as Godzilla. Baragon lumbers off through the countryside, followed by a JSDF helicopter. A hurried cabinet meeting is convened. It is decided to send all resources against this creature, which may be Godzilla. The search mission is scratched.
Yaezu Harbor. An old fishing trawler captain derides a radio report of a red Godzilla appearing on land, angrily stating that Godzilla isn't red. The trawler is suddenly rocked back and forth, then lifted into the air. Horrified fishermen on the dock watch as a mountain of water rises from the harbor. The water falls away, revealing Godzilla. The trawler falls from Godzilla's back, carrying its occupants to their death as it plummets. Godzilla roars, the sound shattering windows on shore.
In the ice cave at Mt. Fuji, Isayama stands, silently observing the slumbering Ghidorah, the statue at the old man's side.
Godzilla lumbers into Shimizu City, smashing the metropolis, crushing fleeing crowds under his feet. News of his appearance throws the cabinet into confusion, wondering which monster report is accurate. In a hospital bed, a survivor of Magonoteh Island watches in horror as Godzilla approaches. Her leg held in traction, she cannot flee. The girl gasps in terrified relief as Godzilla passes. But his tail swings back, smashing the entire floor of the hospital.
The cabinet receives a confirmation that Godzilla is in Shimizu City, destroying the residential areas.
Mobs flee from Godzilla. The beast pauses in his advance, turning to stae down at them. A bright glow gathers in his throat. Far away, a school is preparing to evacuate when a bright flash followed by a shockwave rattles the building. Looking from the window, the teacher can see an atomic mushroom cloud rising in the distance.
Yuri and Takeda drive toward where Baragon is heading. Yuri has brought the stone shard with her. Overhead they see a news helicopter, Yuri tells Takeda to follow it. At the Ministry of Defense, it is discovered that Baragon is heading towards Godzilla. Analysis also shows that Godzilla is definitely heading towards Tokyo, same as the last time.
At Hakone, Baragon rumbles forward, passing beneath a tram-line. Tourists farther away snap photos of the beast, unconcerned. Godzilla's head appears above the hill behind them. The monster claws his way through the hill, crushing tourists beneath an avalanche of stone. Baragon faces off against Godzilla. The Ministry of Defense watches the newscast from the helicopter as they film the standoff.
Baragon burrows under the ground as Godzilla advances. Godzilla looks around, trying to find his enemy. The monster undermines the ground beneath Godzilla and Godzilla falls into the resulting hole. Baragon looses no time, but presses the attack, launching himself at Godzilla from the side of a hill, clamping his jaws on Godzilla's arm.
Yuri and Takeda arrive on the scene, both awed and astonished by Godzilla's size. Baragon is clearly no match. As they watch, Godzilla flings Baragon from him, casting the guardian beast across a parking lot teaming with evacuees and into the side of a hill. Godzilla presses the attack, stomping Baragon's body underfoot, kicking him mercilessly. Baragon manages to escape, climbing up the hill as Godzilla batters him with his tail.
Baragon reaches the hilltop and leaps at Godzilla. Godzilla ducks and batters Baragon away with his tail. The falling monster smashes into the circling news helicopter, destroying it and driving home the mortality of the situation to Yuri. She races to a hilltop observatory that overlooks the battle. She and Takeda watch as Godzilla pauses before Baragon. In a burst of awesome power, Godzilla blasts Baragon, the hill, and a good portion of the observatory with his atomic flame. Baragon flops helplessly as Godzilla sends a second blast of flame searing into him, consuming him utterly.
In the ice cave, the death of Baragon causes the ice imprisoning Ghidorah to crack.
Takeda gets Yuri to a hospital where her injuries are attended. She tries to comfort a young boy, telling him that everything will be okay, there are people fighting for them and that their guardian monster is fighting for them also. When Yuri sees Takeda, the writer refuses to take her after Godzilla, worried about her safety.
Meanwhile at Lake Ishima, a huge cocoon appears.
Yuri arrives at a bike shop as the owner prepares to evacuate. She hurriedly purchases a bicycle so she can follow after Godzilla.
The cabinet appoints General Mikumo as commander over the anti-Godzilla defense. General Mikumo, sure of the strength of their weapons, sends a fighter squadron to stop Godzilla.
Meanwhile, Yuri bikes her way through the mass of refugees. She calls the station, telling them she will broadcast live pictures of Godzilla from her digital camera. Haruki quickly orders that the program they were going to run be pulled and tells Yuri to give him a good show.
The JSDF fighters attack Godzilla in the countryside. Despite direct hits, their missiles have no effect. Incredulous, General Mikumo orders them to try attacking at a steeper angle. Even as the flight commander protests, Godzilla plays his flame across the sky. The debris from the fighters devastates a town as the fiery shrapnel falls.
As Isayama watches, Ghidorah emerges from the ice. At Lake Ishima, the cocoon opens, and Mothra's gigantic form emerges.
Lt. General Tachibana confronts a military politician who reveals to him the JSDF's dirty secret. Fifty years ago it was not their weapons that destroyed Godzilla but a chemical device whose creation is no longer available to them. In order to protect the JSDF's funding, politicians like himself have perpetuated the lie that they killed Godzilla fifty years ago with simple military power.
Yuri continues to transmit. Takeda drives toward Tokyo to stop her, fearing for her safety. Tachibana orders her arrest when he hears the news. General Mikumo is further stunned when Mothra is reported flying toward the Tokyo area.
Touching the stone shard in her bag, Yuri can sense Ghidorah awakening. News that another monster has appeared at Mt. Fuji drives General Mikumo into a rage. Like Mothra, it is reported heading toward Tokyo - toward Godzilla. Through her televised report, Yuri begs the JSDF to fire only on Godzilla, the other monsters have arrived to help. Tachibana is given command of the fleet at his request and he leaves the command center.
In Yokohama, the JSDF prepares for Godzilla's arrival. Meanwhile, Tachibana takes command of the fleet. They will use the D-3 High explosive missiles on Godzilla. On land, missile carriers take aim. Godzilla lumbers into the city, but is at once confronted by Mothra. The JSDF stands down, watching the monsters face off.
Mothra initiates the attack, diving at Godzilla and slashing him. On her return run, Mothra fires a barrage of explosive stingers that topples Godzilla. Enraged, Godzilla rises and fires his ray at Mothra, chasing her across the sky with the beam. Yuri is almost buried in rubble as the beam smashes a nearby building.
Mothra circles and attacks Godzilla again from behind. The ground shakes and Ghidorah emerges in the midst of the city. Mothra backs down and Ghidorah attacks, shocking Godzilla's body with thunderbolts. Tachibana orders the fleet in. He has been waiting for Ghidorah to arrive. They will now act as allied forces with the monsters against Godzilla.
Godzilla breaks away from Ghidorah. Yuri is found and arrested by soldiers.
Godzilla attacks Ghidorah with a vengeance. As Mothra tries to interfere, he swats her away with his tail. With a burst of power, Godzilla swings Ghidorah by his heads, sending the dragon crashing on top of a building. Remorseless, Godzilla blasts Ghidorah with his flame, crippling and stunning him. Lumbering forward to finish Ghidorah off, Godzilla's flame is blocked as Mothra flies between Godzilla's flame and Ghidorah. Mothra is knocked away, plowing through entire city blocks.
The JSDF attacks. From land and sea the D-3 missiles deploy, striking Godzilla. But his hide is too tough for even the missiles to burrow into. The ground forces watch with grim resignation as the unharmed Godzilla turns his flame on them. The losses are hideous, in excess of 90% as Godzilla attacks relentlessly. The fleet is savaged and Tachibana's ship damaged by the assault. Godzilla lumbers toward the bay to finish the job.
From behind Godzilla, her wings burning, Mothra rises once more. Still staring at the ship, Godzilla begins to gather his flame. At the last instant, however, he turns and blasts Mothra before she can attack him. From point blank, Godzilla's fire consumes Mothra, disintegrating her. Godzilla roars in triumph.
Mothra's shimmering energies stream across Yokohama, settling on the wounded Ghidorah. The surge of power revives him and also gives him enough energy to mature. King Ghidorah opens his wings and takes into the night sky. Glowing with power, he flies toward Godzilla. Godzilla blasts the dragon, but King Ghidorah's energy field absorbs the atomic energy and directs it back at Godzilla in a tremendous fireball that hurls Godzilla backwards into the bay.
Injured, Godzilla surfaces, snarling in challenge at the circling King Ghidorah. King Ghidorah answers the challenge, diving at Godzilla, both monsters sinking to the bottom.
Tachibana decides that they will load D-3 torpedoes onto the Satsuma and try to attack Godzilla again by firing one of the torpedoes into the monster's wounds. Captain Kiyose volunteers to pilot the other sub, since each craft can carry only one torpedo.
Underwater, Godzilla and King Ghidorah struggle in hand-to-hand combat. Tachibana's decision to attack Godzilla personally is reported over military radio. Detained by soldiers, Yuri hears the news. The soldier guarding her is in contact with Tachibana and lets Yuri talk to him. Yuri demands to know why Tachibana, a lieutenant general, is going himself. Tachibana responds that it is his duty, would she rather that someone else go? Yuri says it is her job to report the battle, despite the danger. Tachibana relents, telling the guard to let her go, with full authorization to report. Takeda arrives, worried about Yuri and together they hurry to the bridge overlooking Tokyo Bay where the battle is unfolding. Yuri broadcasts once again, honouring all those fighting to protect them all from Godzilla. A stray beam from Godzilla strikes the bridge, causing much of it to collapse. Yuri nearly falls, caught at the last instant by Takeda. However, the writer is not strong enough to pull her back to safety, able only to maintain his hold on her hand.
Down below, the subs close upon the battle. The plan is to strike Godzilla's injury, which is bleeding energy and so can be targeted by heat-seekers. However, as Capt. Kiyose launches his torpedo, Godzilla sees the attack coming. He turns his body around, causing the torpedo to hit King Ghidorah's neck. The detonation further weakens the valiant guardian beast and Godzilla mortally injures King Ghidorah with a point blank blast of radiation. Godzilla then attacks the Satsuma, damaging it badly.
On the bridge, as Yuri dangles over the side, the small stone shard from Mt. Fuji falls from her bag. Sinking into the bay, the shard drifts directly toward King Ghidorah, reviving him with a boost of energy. Sensing his benefactors, Yuri and Takeda falling from the bridge, King Ghidorah roars, causing a burst of bubbles that breaks their fall.
The revitalized King Ghidorah returns to the attack, allowing the Satsuma to escape Godzilla's grasp. King Ghidorah returns to the air, Godzilla surfacing to battle him. The dragon blasts Godzilla relentlessly with energized attacks. But Godzilla retaliates with an awesome point blank blast of destruction. King Ghidorah, his energy faded, is utterly consumed by the blast, chunks of meat raining across the bay.
As the last of the guardian beasts dies, however, the spirits of all three manifest themselves as spectral shadows. The ghostly energies wash over Godzilla, stunning him and causing him to submerge once more.
Tachibana attacks the stunned Godzilla, piloting the Satsuma right down Godzilla's throat. The sub is knocked about within Godzilla's body. A vision of his daughter appears to Tachibana as he lies unconscious at the controls, reminding him why he is fighting. Tachibana recovers from his black-out and leaps into action. Meanwhile, Takeda manages to resuscitate Yuri on the shore of the bay. They watch in horror as Godzilla rises from the bay only yards away from them. However, Tachibana has fired his torpedo. The torpedo burrows its way out of Godzilla's chest from within.
Godzilla turns his ire on Yuri and Takeda, preparing to immolate them with his radioactive breath. Yuri and Takeda brace themselves for death. The blast does not come. The radioactive fire instead bursts from the wound caused by the torpedo. Enraged, Godzilla tries again and this time the rampant energy cripples him and he sinks back into the bay.
The Satsuma escapes from Godzilla's maimed body and as Godzilla tries to blast the escaping sub, his compromised body is at last overcome by the unchecked nuclear energies. Tokyo Bay explodes in a giant commotion of waves as Godzilla's form detonates below the surface like an atomic bomb. In the JSDF headquarters, it is reported that Godzilla is no longer on their radar.
The Satsuma emerges from below. Yuri and Takeda hurry to see her father when Tachibana makes his way to shore. In the JSDF headquarters there is much relief that Tachibana has survived. At Digital BS, Haruki plans a special program when he finds out that Yuri is safe. He plans to use the footage of Professor Isayama, but is shocked when he learns that a background check on Isayama shows that he disappeared in 1954 during Godzilla's attack. He was 75 at the time in any event. Also, the professor has disappeared from all the video tapes.
On the shore, Yuri races to embrace her father. Tachibana warns her back. He must be checked for radiation after his close proximity to Godzilla. Understanding what he means, Yuri salutes her father's sacrifice. Tachibana says that they must honour all the soldiers who gave their lives, and the fallen god-beasts of Yamato.
Beneath the water, amid the rubble and ruin, the disembodied heart of Godzilla lies, slowly throbbing back to life.