A Japanese fishing boat is destroyed by a flash of light near Odo Island, and another ship sent to investigate meets the same fate. The elder at Odo Island blames their poor fishing on Gojira, who they would sacrifice girls to. They perform a ceremony to keep the monster away, but as they sleep, Gojira rises and attacks, killing many.
Archeologist Kyohei Yamane arrives at the island and comes across giant, radioactive footprints. An alarm is sounded, and the natives arm themselves and are attacked by Gojira. After a fight, Gojira leaves back to the ocean.
After Gojira's presence is released to the public, ships are sent to kill him, but they fail and Gojira appears again, causing panic. Officials appeal for Yamane for some way to kill the monster, but Yamane wants to keep Gojira alive to study him.
During the night, Gojira rises from Tokyo Bay and attacks the city. He leaves quickly, but he kills a large number of people. The army constructs an electrical tower to keep Gojira away. However, Gojira breaks through the tower and massacres the city. This results in the city being in ruins, with hospitals overflowing with victims, several having radiation burns. Yamane's daughter Emiko reveals to Hideto Ogata that Daisuke Serizawa has a machine called the Oxygen Destroyer that disintegrates oxygen atoms and orgasms, killing the life form. Serizawa refuses to use the weapon, fearing the military will misuse it. However, when seeing the devastation Gojira caused, he agrees to use it. He burns all his research and eventually uses the Oxygen Destroyer on Gojira as he sleeps, reducing him to bone. Serizawa then kills himself.
Godzilla Mothra and King Ghidorah: Giant Monsters All-Out Attack
Unfortunately, Gojira would be resurrected and possessed by the spirits of dead soilders from WWII who seeked vengeance against Japan for the sins of WWII. Gojira battled Mothra, Baragon, and King Ghidorah, who seeked to save Japan. Gojira killed them all. However, the spirits of the dead monsters possessed Gojira and allowed General Tachibana to fire a submersible into Gojira's throat. When Gojira tried to use his atomic breath, he was torn to shreds, although his heart survived.
Godzilla Against Mechagodzilla and Godzilla: Tokyo S.O.S.
He later returns as the bones to construct the Millennium Mechagodzilla, Kiryu. The malicious influence of this Godzilla turned out still remains within the cloned DNA based on the remaining original DNA within the bones, as when Kiryu activated to fight the new Godzilla, something horrific happened: the cyborg's memories that gained from the remains of the deceased Godzilla were reawakened by the modern Godzilla's own roars. Kiryu broke free of its pilot, Akane Yashiro, and proceeded to trash Tokyo, ignoring attempts at manual override. Godzilla left the city and headed back to the ocean, with Kiryu continuing its rampage until its fuel ran out.
Though Kiryu was eventually put back into control, the Shobijin, Mothra's twin fairy friend, appeared to warn Japan. They claimed that building Kiryu using the bones of the Godzilla that appeared in 1954 was a violation of the natural order of things, attracting the current Godzilla. The twins further claimed that Mothra would gladly take Kiryu's place in protecting Japan if they agreed to dismantle Kiryu, and if they declined, Mothra would attack Japan. Since Kiryu had been built partially to defend against a second attack from Mothra herself, the Japanese declined.
But when Godzilla appeared and killed Kamoebas, Mothra voluntarily engaged him, and Prime Minister Hayato Igarishi was shamed into aiding her. Kiryu flew into battle again. Despite the team up, the current adult Mothra was killed and Kiryu's transmitter damaged once again. Just like Akane before him, Yoshito entered Kiryu for repairs, but remained inside the mech during the battle after Godzilla's beam had accidentally struck both of the hatch doors damaging and jamming it.
Teaming up with the newly-hatched twin Mothra larva, the modified 3-Kiryu was able to use his drill in his right arm to injure Godzilla's chest even more, eventually reaching and tearing up his insides. While Godzilla screamed in pain, Kiryu fired his Triple Hyper Maser and Maser Cannons at Godzilla, making Godzilla's roar trigger another flashback in Kiryu which was directly channeled to Yoshito. Godzilla was then wrapped up by the twin Mothra larva web. Unable to fight, Godzilla dropped to the ground, allowing Kiryu to win the battle. Kiryu then broke free of Akiba's control. Instead of finishing his battle, he merely subdued Godzilla, carrying him out to sea. After releasing Yoshito to safety, Kiryu displayed a message saying "Sayonara Yoshito" on a computer monitor, then plunged into the depths with his organic counterpart, allowing himself to finally rest in peace, while ensuring Godzilla would survive. This marked the first time that MechaGodzilla was able to defeat Godzilla decisively by the end of a Godzilla film without Godzilla coming back to destroy him, and the threat of the first Godzilla finally ended for good.