- Godzilla, the main protagonist of the film, who fights Rodan most of the film, but teams up with him and fights King Ghidorah.
- Rodan, appears in most of the film fighting Godzilla, but later teams up with him and Mothra to fight King Ghidorah.
- Mothra, one of the larvae from the film, Mothra vs. Godzilla (there was another larva, and the Shobijin explain the larva died), and tries to convince Godzilla and Rodan to team up and fight King Ghidorah.
- King Ghidorah, the main antagonist of the film, who first fights Mothra, but then Rodan and Godzilla help out and defeat him.
Write the second Police Detective Shindo is assigned to guard Princess Selina Salno of Selgina 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 the exact same time a meteorite shower draws the attention of Professor Murai, who along with his team of scientists strikes out into the wilderness to examine the largest of the meteors, which has strange magnetic properties.
To Shindo's surprise, the supposedly deceased Selina turns up in Japan, sans her royal garb (including the golden bracelet which 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, who was behind the assassination attempt, learns of her survival and sends his best assassin Malness 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, 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, 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 Venusian as she claims. As if emboldened by the doctor's diagnosis, Selina reveals her final prophecy—that Venus' 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 aide of the Shobijin to summon Mothra. Upon arriving on the Japanese mainland, Mothra attempts to persuade the quarreling Godzilla and Rodan to team up against the evil alien but neither have any interest in helping her rescue the humans who have repeatedly tried to kill them both. Unable to convince them and despite being vastly overpowered, Mothra resolves to fight Ghidorah by herself and is nearly killed before 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 Malmess and his men converge on Tsukamoto's clinic; they fend the killers off and escape into the mountains as the dueling monsters draw closer, so they can watch the battle from a safe distance.
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 Venusian. 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 watch as the combined might of Godzilla, Mothra and Rodan successfully repels the fearsome Ghidorah, sending the three-headed monster fleeing 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.
- The Godzilla suit in this film is called Mosugoji 2, or alternatively, Sandaigoji.
- There is a scene, where King Ghidorah shoots his lightning beams at Godzilla's testicles.
- Godzilla does not use his atomic breath against King Ghidorah in the film, even though it is shown on the Japanese poster.
- This film marks the first Godzilla film to feature Rodan.
- While talking to Mothra, Godzilla states he only hates humans because they hate him, and because of what he perceives as unprovoked attacks towards him, meaning that he was not really a villain in the first place.
The film sold approximately 4,320,000 tickets in Japan.