50 years after Godzilla appeared and was seemingly defeated, the Japanese have grown apathetic to the horror of the monster. Admiral Tachibana, however, maintains a constant vigilance in case Godzilla should decide to return. Sure enough, when inspecting the site of an American submarine disaster, his crew has a close encounter with a new, and very much alive, Godzilla. Tachibana’s daughter Yuri is a reporter for a junk cable station. Although she longs to report on something worthwhile, her station continues to produce one bad program after another. When another monster allegedly appears in Niigata, Yuri digs deeper and learns the legend of the Guardian Beasts, who protect the Japanese lands. It would seem that these Guardians - Baragon, Mothra and Ghidorah - are slowly awakening from their thousand year sleep to protect their land from the threat of Godzilla. She shares her discovery with Tachibana. He’s skeptical at first, but as signs of the other monsters appear, he begins to accept the legend as fact and plans accordingly.

The monster from Niigata, Baragon, surfaces and clambers towards the springs at Hakone. Godzilla itself emerges at Yaizu and heads the same direction. The two monsters clash, but Baragon is no match for the much larger and stronger Godzilla. Baragon is destroyed, but its spirit serves to further strengthen the still sleeping Ghidorah. Yuri tracks Godzilla as it makes it way to Tokyo, where Tachibana has taken command of the counterattack and installed a military base at Yokohama. Mothra appears, having matured from its cocoon at Lake Ikeda, and challenges Godzilla. Tachibana holds off his own attack until Ghidorah itself appears, ready to fight. Godzilla handily defeats both monsters, but has been injured in the process. Tachibana has his men open fire, but only incurs Godzilla’s wrath. Mothra revives briefly, but is obliterated by Godzilla’s heat beam. Mothra’s spirit merges with Ghidorah, granting it renewed power. Ghidorah blasts Godzilla into the bay, where the two monsters continue to fight underwater.

Tachibana loads a drill warhead onto a minisub, and pilots it close to the monsters. Ghidorah and Godzilla surface, where Ghidorah unleashes a barrage of energy attacks as a last resort. Godzilla absorbs the energy and fires it back, killing Ghidorah. Godzilla submerges, where Tachibana pilots his sub into the monster’s mouth and allows himself to be swallowed. Once inside, he fires his warhead into a wound in Godzilla’s shoulder. When Godzilla attempts to use his heat beam, it redirects through his wound, making it even larger. Tachibana escapes as Godzilla’s reckless energy causes him to explode. Yuri and Tachibana reunite on the shore, but at a distance, until he can have his radiation exposure checked. They pay tribute to the guardian beasts who sacrificed themselves to defeat Godzilla.