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.

In 1945, after the horrific fire-bombings of the Pacific War levels Japan to the ground, the government consults spiritual psychics to aid them in winning the war. Unfortunately, the souls' resentment and agony of the victims culminate together to revive the evil Onmyoji, Yasunori Kato. Only a young, psychically imbued priests' apprentice will dare fight the evil magician.