During a meeting of the Japan Self-Defense Forces (JSDF) for the potential return of Godzilla, Admiral Taizo Tachibana briefs cadets about Godzilla’s attack on Tokyo 50 years earlier. A nuclear submarine is reported missing, which is later found to have been destroyed by Godzilla. Tachibana’s daughter, Yuri Tachibana film a docudrama with her crew at Mt. Myoko, where a mysterious earthquake randomly ensues. The odd earthquake returns later that night burying a biker gang and leaving one surviving trucker who witnesses the monster, Baragon.
The next day, Yuri is unable to convince her supervisor Haruki Kadokura to report the incident. The SDF attempts to rescue the buried men using a missile called D-03. The surviving trucker tries to explain to a military official what he saw but can only explain that he believed it was Godzilla. Yuri’s friend, Teruaki Takeda, supports her theory that a monster may have been the cause of the mysterious Myoko earthquake by giving her a book on The Guardian Monsters.
Meanwhile, a few teenagers at Lake Ikeda in Kagoshima are attacked by an insect monster, Mothra. The Defense Force analyzes underwater footage of what appears to be glowing dorsal fins leaving the destroyed nuclear submarine from before. The conclusion is drawn that the monster is Godzilla. Yuri interviews Hirotoshi Isayama, an elderly man who foretells the return of Godzilla. Isayama explains to her the legend of the guardian monsters, Baragon, Mothra, and King Ghidorah and goes on that they must be awakened before Godzilla destroys Japan. Yuri and her team visit the guardian monsters shrine where she finds a stone. Godzilla comes ashore to Magonote and attacks the Bonin Islands, leaving few survivors. Yuri returns to interview Isayama and discovers that the lost souls of World War II are embedded within Godzilla and wish to destroy Japan after the nation forgot their sacrifices.
A few days later, Godzilla and Baragon finally appear in Japan and engage in a ferocious battle in Hakone. Yuri and Takeda are trapped in the midst of the battle when Godzilla mercilessly defeats Baragon with its atomic breath. After the battle, Yuri receives a minor injury to the head. Fearing for her safety, Takeda refuses to take her to Godzilla’s location. Angered, Yuri goes alone. Mothra’s cocoon is soon immediately discovered in Lake Ikeda. The SDF dispatch several fighter jets to stop Godzilla but are quickly defeated by the monster. Tachibana sets up a defense line in Yokohama. Mothra and a yet-to-be-grown Ghidorah awaken and fly towards Yokohama where Godzilla is spotted. Mothra arrives first and battles the monster. Ghidorah arrives moments later and joins the fray. After brutally pinning down both monsters, the SDF engage Godzilla with D-03 missiles; but to no avail, as the missiles fail.
Enraged, Godzilla swiftly destroys nearly the entire defense line using its atomic breath. Mothra rises for a surprise attack, but Godzilla kills her using its atomic breath. Mothra’s spirit intertwines with Ghidorah and transforms it into the 3,000 year old dragon King Ghidorah. King Ghidorah injures Godzilla and takes the battle underwater. Tachibana and his colleague join the fight using the Satsuma submarine. Tachibana plans to shoots a D-03 into Godzilla’s wound but fails after several attempts, even accidentally hitting King Ghidorah with one of the missiles. Yuri and Takeda report the struggle from a bridge that later collapses from Godzilla’s atomic breath.
Takeda and Yuri hold on; however, the shrine stone falls from Takeda’s pockets and sinks into the deep, melting on King Ghidorah’s head. Ghidorah’s power is further enhanced by the stone and the battle returns to the surface. Yuri and Takeda barely survive the fall and swim ashore while the monsters continue to fight. Godzilla destroys King Ghidorah with a super power breath that unleashes the spirits of the Guardian Monsters, which sink Godzilla down to the deep. After entering Godzilla’s body through his mouth, Tachibana successfully plants a D-03 missile in Godzilla’s wound. Godzilla surfaces to come face to face with Yuri and Takeda, and the D-03 punches out from inside Godzilla and explodes, fully wounding him. Still, Godzilla prepares to atomic blast Yuri and Takeda, only to have the energy redirected through the missile hole, expanding the wound and causing the great beast to sink once more beneath the water. Tachibana exits Godzilla’s body through the monster’s wound right before the monster disintegrates. Japan soon rejoices at their victory against Godzilla. The only thing left alive of the monster is its heart, still beating on the ocean floor.