WARNING: Contains nothing but spoilers
A group of sailors in a ship called the Eiko-maru are partying until a flash of light blinds them, turning into a burning wreck. Before the ship sinks, a morse code is sent before sinking to the bottom of the ocean.
Our two main characters, Hideki Ogata and Emiko Yamane, are to cancel their date as Ogata is called by his company to find the missing Eiko-maru. Another ship, Daigo-maru is dispatched to find survivors, but it too, faces the same fate. Tension rises as worried families and friends are in constant peril. However, a fishing boat finds two survivors, only to again face the same fate.
In Odo Island, a group of fishermen are in a food drought, until the villiage elder believes Gojira (Godzilla) is behind it. A young reporter tries to interview several people, including the survivor Masaji, who mentions seeing a monster.
At the night, the village elder explains an exorcism ceremony is to appease the monster Godzilla, while previously had done with young virgins. As the night looms and a typhoon storms, a mysterious sound hits the island. A young boy, Shinkichi, survives this fateful encounter leaving his brother and mother dead, and he is the only one who saw the cause.
Back in Japan, a conference is held concerning the event that killed several people and damages to the island. A paleologist, Kyohei Yamane, leads an exhibition to find out what has happened to the island.
As scientists investigate the island, Dr. Yamane and his fellow scientists finds the area is polluted with radiation, and finds a miraculous discovery: A trilobyte is found amongst the destruction. The village alarms the people of a monster, a giant dinosaurian monster bellows the people below as they retreat. The monster retreats to the ocean as the scientists return to Japan with this horrifying discovery.
Dr. Yamane holds another conference concerning about the creature he calls Gojira (Godzilla), explaining the monster may have been awakened by a nuclear test in the Pacific. Post conference, one politician believes the The Reveal should be kept secret while a female politician believes this secret should be opened to the public. Arguments ensue and they succeed. To ensure safety, the Japanese military is dispatched to destroy the monster. Dr. Yamane, sadden by the government's decision to destroy the monster, sits alone in the dark. Meanwhile a group of partygoers are celebrating. However, to their horror, Godzilla survives the attempt to kill him. The patrons retreats while Godzilla dives in the ocean.
The government holds a third conference with Dr. Yamane asking his opinion on how to kill Godzilla. The already dishearten professor believes Godzilla cannot be destroyed as he survived a nuclear testing. He then advises a scientific approach to be used. Meanwhile Emiko and Ogata are discussing about their friend, Daisuke Serizawa, whom Emiko had her Arranged Marriage to. A reporter Hagiwara, requests to interview Serizawa. Emiko takes the chance to see him to break up their arrangement.
We meet Serizawa, a young man with an eyepatch and a scar, who denies everything in his interview. Afterwards, he takes Emiko to his basement laboratory. Serizawa uses an unknown object for a demonstration. Emiko sees, then realizes its horrific use. Serizawa then tells her to promise to never reveal about his secret invention and she complies. Back in Yamane's household, Godzilla makes his entrance. Dr. Yamane warns to never shine lights at Godzilla, however the military are too busy with evacuating civilians to safety. As Godzilla is rampant in a trainyard, he picks up a trains and throws it to the ground. While short, Godzilla leaves a substantial destruction and death before leaving in the ocean.
The government then enacts a plan to destroy Godzilla by using high-tension electrical towers should he surface again. Civilians are evacuated in shelters and the military are waiting for him to rise. Later, Ogata intends to ask Dr. Yamane to take Emiko's hand. The dishearten doctor only wants to research the monster while Ogata agrees with the government to destroy Godzilla. Angry, Dr. Yamane kicks out Ogata from his house. Godzilla rises again, this time the military being prepared. As Godzilla crosses the towers, the military bombards the monster with everything they have, until they discovered another horrifying discovery: The monster has a radioactive Breath Weapon.
After destroying the towers, Godzilla proceeds in destroying the city of Tokyo, sentencing thousands of people to death. The military in vain, tries to fight back, but conventional weapons proves to be an annoyance to him. The military had no choice but to rescue survivors as they can while Godzilla rampages. A news crew angers the King of the Monster with their flashing lights and Godzilla sends them to their deaths. The remaining survivors look on as Godzilla reduces Tokyo into a burning city. However fighter jets are sent to face Godzilla as a last ditch effort to stop him. After his rampage, Godzilla escapes to the sea.
After Godzilla leaves, the remaining survivors are forced to treat the injured as well as the dying. Others fell victim to radiation poisoning. Having enough of the terrible sight, Emiko is forced to tell Ogata the promise she made to Serizawa...
Serizawa shows Emiko his terrible creation, the Oxygen Destroyer, which can kill all organisms in the water by asphyxiating them. Serizawa, who was devoted in researching the element of oxygen, found this terrible power by accident. He then decides to keep the Oxygen Destroyer a secret, and should he does so, he would burn the notes at the event of his death, and Emiko promises to never reveal its existence...
Ogata, uplifted by this news, decides to see Serizawa about the Oxygen Destroyer. Serizawa denies its existence, but Emiko breaks down having broken her promise. Serizawa angrily refuses to give up his Oxygen Destroyer, and he and Ogata scuffle, resulting in Ogata having a bleeding forehead. Having a My God, What Have I Done? realization, Serizawa helps Ogata and tells him because of what it is, the Oxygen Destroyer is nothing but another weapon of mass destruction. With the terror of Godzilla and the potential of an arms race with the Oxygen Destroyer, Serizawa is in a forceful dilemma. However, a news broadcast showcases the destruction Godzilla. Realizing this, Serizawa then burns his notes as Emiko breaks down remembering what he said.
The military locates Godzilla and Serizawa volunteers to dive in the ocean. Ogata protests, but reluctantly goes with him to find Godzilla. As the divers sink, Godzilla has awaken from his peaceful rest as Ogata and Serizawa look for him. As the divers find him, Ogata surfaces but realizes Serizawa remains at the bottom. Seeing Godzilla up close, Serizawa detonates the Oxygen Destroyer and Godzilla dying. In the surface, Ogata shouts for Serizawa. However, Serizawa does respond when the Oxygen Destroyer worked. His last words is for Ogata and Emiko to be together. He then pulls out a knife and cuts his airhose.
As Godzilla rises, he leaves out a dying, yet deafening, roar as he sinks to the bottom of the ocean, reduced to bones, then to nothing. After the monster's death, it leaves nothing but gloom. Ogata tells Emiko that Serizawa wanted them to be together, and she breaks down. Dr. Yamane could not believe Godzilla was the last member of his own species, but if nuclear tests continue to be conducted, another Godzilla might appear somewhere in the world again. The film ends with people on a ship salutes the late Daisuke Serizawa.
