After the previous Godzilla attack, a miniature arms race ensues to collect his cells. Concerned over Godzilla's possible return, the Japanese government uses the cells to create a new bio-weapon, ANEB (Anti-Nuclear Energy Bacteria). They seeks the aid of geneticist Genshiro Shiragami, who's experiments result in a new mutation.

Wishing to find peace, Zatoichi travels to his old village but only finds trouble when he ends up in a love triangle and finds old scores have followed him home.

After arriving in the town of Shimonita, Ichi finds that a price has been put on his head by a local yakuza boss. He's drawn into a trap, but after hearing of the slaying of a former love, Ichi furiously fights his way through the entire clan to face the killer, a hired ronin.

Zatoichi is sworn to protect the life of a young girl and without any real allies finds himself in the middle of a bloody turf war.

A submarine expedition to salvage the remains of Mechagodzilla is thwarted by a massive dinosaur named Titanosaurus. An Interpol investigation leads biologist Ichinose to uncover the work of Dr. Mafune and his mysterious daughter Katsura. Aligned with the Black Hole Aliens, Katsura's life becomes entwined with the resurrected machine.