Police Detective Shindo (Yosuke Natsuki) is assigned to guard Princess Selina Salno of Selgina (Akiko Wakabayashi) during the Princess’ visit to Japan, due to a suspected assassination plot. Although Shindo is smitten with Selina’s photograph, her plane never makes it to Japan, as it is destroyed by a bomb en route. At exactly the same time a meteorite shower draws the attention of Professor Murai (Hiroshi Koizumi), who along with his team of scientists strikes out into the wilderness to examine the largest of the meteors, which has magnetic properties.
To Shindo’s surprise, the supposedly deceased Selina turns up in Japan, without her royal garb (including the golden bracelet that proves she is heir to the throne of Selgina), claiming to be from the planet Venus, and preaching to skeptical crowds of forthcoming disaster. To their surprise however, her prophecies begin coming true. First she predicts Rodan, thought dead in the eruption of Mt. Aso, will emerge from Aso’s crater. Subsequently, none other than Godzilla will arise from the sea and destroy a ship. Both of these events transpire.
In the meantime, Selina’s uncle (Shin Otomo), who was behind the assassination attempt, learns of her survival and sends his best assassin Malness (Hisaya Ito) to Japan to dispatch the Princess and steal the golden bracelet. Malness and his henchmen are stopped by Shindo, who was warned of their attempt by the Shobijin (Emi and Yumi Ito), who were in Japan appearing on a television show. The Shobijin had been scheduled to return to Infant Island aboard the ship sunk by Godzilla, but opted not to go after overhearing Selina’s prophecy. A further attempt by the assassins is thwarted when both Godzilla and Rodan attack the city and engage in battle, forcing everyone to flee.
Convinced that Selina is insane, Shindo takes the Princess to see a renowned psychiatrist, Dr. Tsukamoto (Takashi Shimura), in the hopes of curing her. However, Tsukamoto can find nothing wrong with her, mentally or physically. He concludes she must therefore truly be possessed by a Martian as she claims. As if emboldened by the doctor’s diagnosis, Selina reveals her final prophecy—that Mars’ once thriving civilization was destroyed by an evil, golden three-headed dragon named King Ghidorah, and furthermore that Ghidorah himself has already arrived on Earth. No sooner has she revealed this than Professor Murai and his colleagues at the meteor crash site receive a nasty surprise—the “meteor” is actually an egg, which hatches into the fearsome King Ghidorah. Ghidorah begins razing the countryside.
To combat the combined threats of the three monsters, the Japanese government enlists the aid of the Shobijin to summon Mothra (the surviving larvae from the previous film). Upon arriving on the Japanese mainland, Mothra attempts to persuade the quarreling Godzilla and Rodan to team up against the evil alien (which is translated to the humans by the Shobijin) but both refuse, with Godzilla stating they have no reason to save mankind as both he and Rodan “have always had trouble with men and men hate them”, to which Rodan agrees. Despite Mothra stating that Earth belongs to them as well and that it is their duty to defend it, Godzilla and Rodan still refuse and the pair refuse to forgive each other, wanting to continue their fight. Unable to convince them and despite being vastly outmatched, Mothra calls the pair of them “bullheaded” and resolves to fight Ghidorah by herself. Mothra engages Ghidorah and is continually blasted by his gravity beams. Fortunately for Mothra, Godzilla and Rodan, impressed by her courage and selflessness, arrive to help, and a titanic battle against Ghidorah begins. Meanwhile, Shindo and Dr. Tsukamoto are forced to protect Princess Selina as Malness and his men converge on Tsukamoto’s clinic; they manage to fend off the killers and escape into the mountains as the dueling monsters draw closer.
The assassins attempt to follow, but a stray blast from Ghidorah buries their car in an avalanche. Only Malness remains uninjured enough to continue. He attempts to snipe the Princess from an elevated position, but only injures her. In her pain, she regains her memory and is no longer possessed by the Martian. Before Malness can take another shot, another stray blast from Ghidorah buries the assassin under a second avalanche. With the heroes thus saved from the human menace, they gather at a safe distance to watch the battle between earth’s monsters and Ghidorah. After now gaining a clear advantage over Ghidorah, the three monsters coordinate their attack; Godzilla grabs hold of Ghidorah’s tails while Mothra (riding on Rodan’s back) sprays the three-headed dragon with her silk. Finally, Godzilla throws the alien beast off the cliff and the battered dragon flies off, back into outer space.
As Mothra and the Shobijin return to Infant Island while Godzilla and Rodan go their separate ways, Selina, having retained the memories of her time with Shindo, bids farewell to her guardian as she meets her bodyguards at the airport to return home.