JSDF pilot Akane has a fateful encounter when a new Godzilla emerges in Tateyama. As a countermeasure, a cyborg named Kiryu is constructed from the remains of the original. The machine is discovered to harbor the restless soul of the original monster as Akane must learn to find value in her own life as well.

Japan is thrown into a panic after several ships are sunk near Odo Island. An expedition to the island led by Dr. Kyohei Yamane soon discover something far more devastating than imagined in the form of a 50 meter tall monster whom the natives call Gojira. Now the monster begins a rampage that threatens to destroy not only Japan, but the rest of the world as well.

The advertising director of Pacific Pharmaceuticals, frustrated with the low ratings of their sponsored TV program, seeks a more sensationalist approach. He orders his staff to Faro Island to capture King Kong for exploitation. As Godzilla re-emerges, a media frenzy generates with Pacific looking to capitalize off of the ultimate battle.

Searching for his brother, Ryota stows away on a boat belonging to a criminal alongside two other teenagers. The group shipwrecks on Letchi island and discover the Infant Island natives have been enslaved by a terrorist organization controlling a crustacean monster. Finding a sleeping Godzilla, they decide to awaken him to defeat the terrorists and liberate the natives.

Struggling to elevate himself from his low caste in 17th century Japan, Miyamoto trains to become a mighty samurai warrior.

After years on the road establishing his reputation as Japan's greatest fencer, Takezo returns to Kyoto. Otsu waits for him, yet he has come not for her but to challenge the leader of the region's finest school of fencing. To prove his valor and skill, he walks deliberately into ambushes set up by the school's followers.

A humble and simple Takezo abandons his life as a knight errant. He's sought as a teacher and vassal by Shogun, Japan's most powerful clan leader. He's also challenged to fight by the supremely confident and skillful Sasaki Kojiro. Takezo agrees to fight Kojiro in a year's time but rejects Shogun's patronage, choosing instead to live on the edge of a village, raising vegetables. He's followed there by Otsu and later by Akemi, both in love with him. The year ends as Takezo assists the villagers against a band of brigands. He seeks Otsu's forgiveness and accepts her love, then sets off across the water to Ganryu Island for his final contest.

A burning Godzilla, on the verge of meltdown, emerges to lay siege to Hong Kong. At the same time horrifying new organisms are discovered in Japan. These crustacean-like beings are seemingly born of the Oxygen Destroyer, the weapon that killed the original Godzilla.

The legendary empire of the lost continent of Mu reappears to threaten the world with domination. While countries unite to resist, an isolated World War II Captain has created the greatest warship ever seen, and possibly the surface world's only defense.

Sazae finally gets married, but right after that, Masuo is transferred to Osaka. A heartbroken Sazae sends her parents on a silver wedding trip, and eventually heads for Nikko, a travel destination. Sazae is once again overwhelmed by the sight of the newlyweds bustling with sunlight, but...