Nineteen sixty-five, It's been one year since Godzilla, Mothra and Rodan defeat King Ghidorah.
Godzilla and Mothra were sleeping in their cave, next to each other.
Japanese government figure out that Godzilla only comes to Japan to check on the city like a guardian or wanting to be feed on radiation from nuclear power plants.
They started launching nuclear missiles at him, which kept him out of the city.
Godzilla and Mothra most of day lay in their cave or play rock ball with each other.
The World Space Agency discovered a new planet beyond Jupiter that they call Planet X.
The agency sent two astronauts, Glenn and Kazuo Fuji to investigate Planet X.
While they are gone, Fuji's younger sister, Haruno became romantically involved with inventor, Tetsuo Tori, who has just sold his invention that he named The Lady Guard alarm, to a toy company's CEO named Namikawa.
Glenn and Fuji's spaceship, the P-one, finally arrives on Planet X.
Fuji leaves the ship and goes plant the American and Japanese flags on a nearby hill.
A violent lightning storm passes overhead.
He returns to the landing site after finding human footprints, to find the P-one and Glenn gone.
A tubular elevator ascends to the surface telling Fuji to enter.
Fuji ask "who's talking?"
The voice replies "we are called Xiliens."
He gets in the elevator and is transported to an underground complex and follows the light in the dark to a room where Gleen is seated.
The room lights up and several men dress in black bodysuits with black visors over their eyes enter.
They sit across from the two men.
One of them introduces himself as the Controller of Planet X.
He tells the two men "we would like to discuss some business" when he is informed that 'Monster Zero is attacking'.
Fuji and Glenn ask "who is Monster Zero?"
The Controller shows them a video feed of the space monster, which Glenn and Fuji recognize it as King Ghidorah.
The Controller tells them "you Earthlings give all things names, while we Xiliens give them numbers."
The Controller is informed that a 'hydrogen oxide plant was damaged in Monster Zero's attack'.
He tells them "we are aware that Monster Zero attacked Earth and was driven off by Monster Zero one and Monster Zero two: Godzilla and Rodan, and we ask to borrow them in exchange, we will provide humanity with a cure for cancer."
Glenn and Fuji replies "we don't know were Godzilla or Rodan are."
The Controller answers "Godzilla is on Infant Island or sleeping in the ocean off the coast of Infant Island, while Rodan is sleeping underground on an island called Monster Island."
He ask them "can you you talk to your leaders?"
Glenn and Fuji leave in their P-one.
The Japanese leaders welcome the Xiliens' proposal, but Glenn and Fuji are uneasy about the Xiliens' true intentions.
They meet Haruno and Tetsuo in a restaurant.
Fuji disapprove of Tetsuo dating his younger sister.
Glenn and Fuji leave the restaurant.
Tetsuo looks out of the window to see Glenn leave with Namikawa.
Tetsuo visit the World Education Corporation office to ask about his payment, but is turned away.
Later in the next day, Glenn takes Fuji to lake Myojin.
He tells him "I swear I saw the Controller while at the lodge with Namikawa and hear him say all preparations are complete."
Namikawa complained that Glenn was groaning all night due to them kissing.
JSDF surrounded the lake Myojin.
The head of platoon explains that there is activity in the lake.
A UFO emerges out of the lake.
By daybreak the UFO was joined by two others.
The Controller emerges from the lead ship and holds a meeting with Japanese officials, including Glenn, Fuji and their superior from WSA, Dr. Sakurai.
The Controller apologizes for operating on Earth without their knowledge, but reiterates the urgency of their situation.
The other UFOs seek out Godzilla and Rodan.
The Controller requests that Glenn, Fuji and Sakurai accompany them to oversee the operation.
Before Glenn leaves, he kisses Namikawa goodbye.
Tetsuo sees Namikawa drive off and decides to tail her.
He follows her to a lone house.
He approaches the door, when a trap door opens underneath him.
(with the UFO)
They arrive on Planet X.
Godzilla and Rodan are deposited on the surface, while the others watch from the underground complex.
After the tractor field around them dissolved, they wake up and are attacked by King Ghidorah, who flies overhead and blast them with his gravity beams.
Godzilla and Rodan join forces and fight back.
Godzilla tackles Ghidorah to the ground and blast him with his atomic fire beam, forcing Ghidorah to retreat.
The Controller remarks "this is the first time we defeated Monster Zero."
He turns around to see Glenn and Fuji gone.
Glenn and Fuji explore the complex when they find themselves pursued.
They jump on an elevator which takes them to a grotto on the surface.
There they find plentiful deposits of gold.
Glenn sees an identical female Xilien who looks like Namikawa and approaches her.
When she doesn't recognize him and backs away.
Glenn looks confused until he sees another identical female Xilien approach.
Next, they are surrounded by several armed Xiliens and taken back to the Controller.
The Controller ask "why did you wondered off without permission?"
They reply "we wanted to see more of the planet."
The Controller ask "what did you learn?"
Fuji replies "water is more precious than gold."
Glenn ask "why do all the women have the same faces?"
The Controller rhetorically ask "Glenn, do you admire beautiful faces?"
Glenn replies "beauty is individual."
The Controller replies I will not get in a debate over women's beauty!"
The Controller presents them with a tape that contains the cure for cancer, then sends them back to Earth in a superior replica of the P-one that the Xiliens constructed.
As they left, Glenn and Fuji see Godzilla and Rodan watch them leave.
Fuji, Glenn and Sakurai return to Earth triumphantly and insert the tape into a player before the Japanese government.
The tape starts playing "Earth is to surrender and become a colony of Planet X. In addition, we have control over both Godzilla and Rodan as well as King Ghidorah."
Glenn heads to the World Education Corporation office to confront Namikawa, who is wearing Xilien attire.
He ask "was our relationship part of your plan?"
She replies "I was only suppose to observe you, but I fell in love with you."
Glenn widen his eyes "is that how you beat the Xiliens?"
Namikawa sighs "we aren't allow to love, but you change me for the better."
Glenn realizes he knows how to free Godzilla from mind control.
Namikawa tells him "we Xiliens are vulnerable to a certain sound device I bought and it's too late to fight back. I also want to marry you."
Soon several armed Xiliens entered the room.
They take Glenn to a cell where he encounters Tetsuo.
He tells Tetsuo "the Xiliens are vulnerable to a certain sound from your invention."
Tetsuo activates his Lady Guard alarm.
The Xilien guards run to their cells screaming in agony.
Glenn and Tetsuo escape after getting the keys from the guards.
Glenn and Tetsuo swim back to city.
When they arrive at JSDF headquarters, they inform them of the Xiliens weakness.
The Controller is forced to start the invasion plan early.
Godzilla and Rodan rampage through Japan.
Glenn leaves and heads to Infant Island to get the Queen of monsters, Mothra.
An hour later, Glenn returns with Mothra who confronts Godzilla.
Godzilla stops rampaging through Japan when he sees Mothra.
Mothra chirps "I love you" and touch mouth to mouth in a kiss.
Godzilla shakes his head and fires his atomic fire beam at the UFOs destroying them and their Earth base.
After the mind control is broken, Godzilla, Rodan and Mothra defeat King Ghidorah and send him back into space.
Namikawa leaves the Xiliens and marries Glenn.