A ship is at sea, the crew relaxes on deck as night begins to fall. Near the ship a flash of light baths the ship. Instantly the ship explodes and begins to sink.
Next morning Hideto Ogato (Akira Takarada) receives a phone call. Being a salvage expert the coast guard wants him to report immediately as a result of the sinking.
A situation room is set up to investigate the sinking of the Eiko Maru. Its last position is known but the cause of the sinking is still a mystery, though an explosion is suspected. A rescue vessel "Bingo Maru" approaches the location of the sinking. Again a flash of light erupts out of the water and the Bingo Maru suffers the same fate as the Eiko Maru.
The Coast Guard assures frantic families of the crews of the two ships, that everything is being done including more ships and helicopters committed to the search. Finally there are results as three survivors are found in the water. At the same time reports of the sinking of a fishing boat brings the total of lost ships to three.
On Odo island, the port of the missing fishing boat, inhabitants are scanning the sea looking for signs of the boat. A raft is seen with Masaji Sieji (Ren Yamamoto) who lives on the island on board. The islanders pull the raft in Masajis says "A monster did it" And passes out close to death.
Days later other fishing boats return to the island, complaining their nets are all empty. One of the elders claims it is Godzilla eating the fish. Other members of the village laugh at his quaint ways. The same day a helicopter lands on the island carrying a group of press and military - they interview Masajis who again claims it was a monster. The elder gets their attention and tells the legend of Godzilla. He then explains the history of sacrifices the island used to make to keep Godzilla happy. Now all that is left is the religious ceremony.
During the night a typhoon hits the island. The islanders take shelter but along with the normal noise of such storms they can hear something huge moving around. The next morning 12 houses are found to have been destroyed during the night and at least 9 people have died. Discussions between the mayor and eyewitnesses uncover the fact that the destruction of the houses was unusual, and not caused by the storm.
Professor Kyohei Yamane suggests a scientific task force go to the island to investigate the situation. As the vessel leaves, a number of passengers are surprised to see the reclusive Dr Serizawa (Akihiko Hirata) at the dock to see the expedition off.
At the island the team gets to work, first they detect radiation around the ruined buildings and in the water wells. A series of huge shallow depressions are measured. It becomes apparent the depressions are giant foot prints. In one of the depressions they find a trilobite - a creature extinct for millions of years.
On the other side of the island an alarm sounds, loud rhythmic thunder can be heard approaching. Many realize it is the same sound heard during the storm. The villagers start to climb the island's central ridge to see what is going on.
A huge reptilian rears up and roars at the villagers and disappears. The villages continue towards the creature only to see it disappear into the ocean leaving a series of tracks along a beach.
At a meeting convened to discuss the expeditions findings, Professor Yamane surmises Godzilla is a relic from the age of dinosaurs and has been disturbed by recent hydrogen bomb tests in the Pacific. He displays the trilobite and the radioactive sand found on the island as proof of his argument. Newspaper reports claim that up to 17 ships have been lost because of Godzilla. A special agency is set up to look into ways to counter the creature before all international trade is stopped with Japan. The Japanese navy goes into action depth charging any areas Godzilla was last seen.
In Tokyo Bay a pleasure boat full of party goers sees Godzilla, rather than attack the boat, the creature seems intent on heading for shore. Professor Yammi struggles with the situation. He understands Godzilla needs to be destroyed but feels the creature deserves to live. After all it was man who disturbed and created the creature. He wants to understand what caused things to turn out the way it did.
Orgata speaks to the professor Yammi's daughter and asks her to try and talk to talk to Professor Serizawa who is rumored to have a device that could destroy Godzilla. Newspaperman Hagiwara (Sachio Sakai) asks if he can come along to get a better idea of the true story.
Serizawa is puzzled at the reporters questions. He denies such a weapon exists, but refuses to say what he is really working on. Emiko waits for the reporter go then presses Serizawa for more information, he relents and shows her what he is doing, but she has to be sworn to secrecy first. In the lab Serizawa shows her a process that turns a tank full of fish to skeletons in mere seconds.
Emiko is shocked but validates her promise to Serizawa by not saying anything to Orgata when she returns home. Outside the house sirens sound, and the trade mark thundering steps can be heard in the distance. Godzilla nears the shore and the army opens fire with all the heavy weapons they can muster. Ignoring the armys efforts Godzilla comes ashore destroys a train, then moves into the downtown area. After a protracted battle with the army, the monster destroys a major bridge before heading back to sea.
Next morning newspapers are full of images and stories of the attack. It is noted that scientists from all over the world have begun flying in to help defeat the creature. Quickly it is decided to evacuate the coastal areas around Tokyo Bay. Once this is completed an electrified barrier is to be built. Its hoped that by repeated electrocution Godzilla will be turned away and forced back to sea permanently.
Now that a plan of action is in place Orgata decides now is a good time to ask Professor Yammi for his daughter Emikos hand in marriage. Yammi is completely uninterested in the advance. He is consumed with questions about Godzilla. Frustrated Orgata starts debating Yammi, ultimately Yammi throws him out of the house dashing Emikos hopes.
At nightfall Godzilla is again seen heading for the shoreline. The newly installed electrical barrier is charged and the army takes up position with heavy artillery and tanks. As Godzilla pauses at the barrier the army sees its chance again attacks. Godzilla responds by setting huge fires across the city with its to date unseen radioactive breath.
Realizing their plan has failed the authorities initiate code 129 This means rather than fight Godzilla they are only going to concentrate on getting civilians out of harms way. As the plan takes affect a wing of Japanese fighter craft try to distract the creature. Unexpectedly the attack seems to work and Godzilla retreats back to the waters of Tokyo Bay.
Rescue efforts switch to high gear, but the sheer numbers of wounded, many suffering radiation sickness completely overwhelm hospitals. Despite their best effort the government knows there is little hope for survivors.
Seeing the carnage Emiko confesses to Orgata what she really saw in the Professors lab There really is a way to destroy the creature. She goes on to describe how Serizawa dropped a device into a tank of fish, seconds later all the fish were just skeletons. Serizawa explains how the device sucks all oxygen from water causing any living creature caught by the process to liquefy instantly.
Hearing this Orgata and Emiko agree to confront the Serizawa and convince him to use his discovery. Serizawa counters that to reveal the weapon to the world would unleash a force greater than even the atomic bomb. The only difference is the oxygen destroyer could ultimately kill all mankind.
Serizawa is concerned that once the he uses the weapon the genie is out of the bottle and he does not know if he can get it back in. Serizawa is torn by his choice, but he cannot see any way to resolve it. He catches a sight from the TV of people all over the country praying that Godzilla wont return. He realizes he must act and deploy the weapon.
With a new sense of purpose he begins to destroy data and equipment in his lab notes.
At sea a ship with Orgato and Serizawa aboard a ship mounted with Geiger counters locates Godzilla. Orgata prepares to make the dive to deploy the weapon. Serizawa insists he goes with him. They only have one chance and one weapon, so it has to be done properly. Reaching the ocean floor they find Godzilla resting and begin the work to deploy the weapon. Serizawa unexpectedly signals Orgata to return to the surface. Reaching the surface alone Orgato realizes he has been fooled and Serizawas solution was to die deploying the weapon.
With one final message Serizawa tells Orgata that the weapon worked and he hopes he and Emiko with be happy together. The weapons effect envelopes Godzilla. The creature struggles for a time before sinking to the bottom uttering one final defiant roar. Moments later nothing remains but a skeleton. Within minutes this is gone too
Onboard the ship Professor Yammi considers the concept that there must be more Godzillas out in the depths of the ocean. If man continues his experiments with atomic weapons, chances are extremely high another Godzilla will return to once again threaten our civilization.