Nineteen seventy-two, a year after Godzilla and Mothra beat Hedorah.
Mothra stayed at home while Godzilla left Japan territory after sensing a disturbance somewhere and travel the world.
He returned after a week of tracking the disturbance to an iguana nest destroyed with busted eggs and one cracked open.
Godzilla visit Ken in Suruga Bay and helping them clean up the bay.
In Japan, a freelance manga artist, Gengo Odaka, applies for a job as a designer for Tokyo's World Children's Land, a theme park whose key attraction is a life size replica of Godzilla and he got the job.
Gengo curious about his new job and his boss, Kubota, who is obsessed over world peace despite building monsters for the park.
The organization's Chairman is a seventeen year old boy named Fumio Sudo.
Gengo first meets him, he is charting interstellar coordinates including an Alien race M Space Hunter Nebula.
One day, Gengo bumps into a young woman causing her to drop a magnetic tape.
She scrambles off in a hurry.
Gengo hides the tape from Kubota and other pursuers.
Kubota tells him "that girl is an enemy ofit peace who is trying to foil the park's plans."
Later at night, the young woman he bump into earlier requests "I need that tape back."
Gengo refuses to hand over the tape.
The young girl's companion sticks a corncob in his back causing him to faint.
He wakes up to the boy and girl taking care of him.
The boy introduced himself as Shosaku Takasugi.
The girl introduced herself as Machiko Shima.
Machiko tells him "I'm looking for my brother, Takeshi Shima, a computer technician that works for that organization you work for. The tape you have, is my only clue to his disappearance."
Gengo believes them and snoops around the Godzilla tower for clues.
Gengo manages to find Takeshi locked in a room in the tower and briefly contacts him and unknowingly arouse suspicion from Kubota.
The trio decides to investigate the park's origin's and histories of Sudo Kubota.
They play the stolen tape on Gengo's reel-to-reel player to hear electronic noises.
The signal is picked up by the tower's computers.
The Chairman orders a change of Action Signal Tapes.
The signal is heard by Godzilla and Mothra on Infant Island.
Anguirus also heard the signal on an island and goes check it out.
Gengo and Shosaku investigate Sudo and Kubota and discover that both of them died one year ago in a mountain climbing accident.
Anguirus stop at Tokyo Bay to see nothing wrong and JSDF line along the bay.
Gengo burns the cigarettes outside in the yard.
Kubota sends two men to capture them.
Gengo's girlfriend, Tomoko Tomoe, a black belt in karate, beats the intruders and drives them away.
Gengo tries getting the police to help them, but are turned away.
Gengo and Tomoko break into the tower and try to sneak Takeshi out at night.
Their plan backfires and Gengo and Tomoko get captured.
Kubota reveals that "me and the Children's Land staff are aliens from the M Space Hunter Nebula. Our goal is to take over Earth.
We use the tapes to command the space monsters, Gigan and King Ghidorah to level Tokyo."
Godzilla and Mothra arrives at Tokyo Bay to see Anguirus waiting and JSDF line along the bay.
Gigan and King Ghidorah arrive and begin laying waste to Tokyo.
Godzilla roars at the space monsters and writes in sand 'need a nuke for a power boost'.
Godzilla and Mothra battle King Ghidorah while Anguirus battles Gigan.
Godzilla punches Ghidorah's right head while cuffing the left head.
Mothra blast Ghidorah with her energy beams.
Anguirus charges at Gigan before rolling into a ball and hitting Gigan with the spikes on his back.
General of JSDF reads Godzilla's note and orders the Japanese navy to check for nukes in their inventory of weapons to power Godzilla.
The aliens blast Godzilla with laser beam from the tower, which is immensely effective against Godzilla.
Shosaku and Machiko rescue Gengo, Tomoko and Takeshi from the tower.
Mothra then fires her energy beams at the tower, destroying it completely.
Gengo looks at Mothra wondering what the relationship between the moth and Godzilla is.
A JSDF soldier tells him "they are the King and Queen of all monsters and they will come to the aid of each other when needed."
Tomoko points out "that's weird for their relationship."
Gigan tries buzz saw through Godzilla.
King Ghidorah resorts back to trying to shape the world to his liking.
Anguirus tries to fight back against King Ghidorah.
Mothra blast King Ghidorah with her energy beams.
Godzilla fires his atomic fire beam at Gigan.
King Ghidorah blast Mothra with his gravity beams burning her wings.
Godzilla release a powerful blast of his atomic fire beam at Ghidorah, knocking Ghidorah down.
Anguirus ran into Gigan again.
Tomoko gaped "Godzilla is down."
JSDF launch a nuke at Godzilla giving him power.
Mothra chirps "beat them my King."
Godzilla absorbed the radiation from the nuke and started firing his red atomic fire beam at King Ghidorah and Gigan.
Ghidorah blast Godzilla with his gravity beams but didn't phase Godzilla.
Godzilla unleashed a nuclear pulse at them burning them.
Gigan sensing that he can't beat them flee into space.
King Ghidorah followed after Gigan into space.
After they left, Godzilla picked Mothra up and carried her to sea.
Anguirus returned to an island.
Mothra rode on Godzilla's back to Infant Island to sleep.
Gengo and his group look on as the three Earth monster leave Tokyo.
Tomoko points out "Godzilla and Mothra have a weird relationship with each other."
Godzilla and Mothra arrive home on Infant Island and walked to their cave to sleep.
Godzilla laid down on his side and Mothra snuggled into him.
Mothra chirps "I love you Gojira."
Godzilla moans "I love you too, Mosura."