Japan, 250 years ago. Soetsu is a moneylender who is killed by the cruel samurai Shinzaemon. His body is dumped in the Kasenega-Fuchi river. According to legend, all who drown in the river will never surface again. 20 Years later, Shinkichi, the handsome son of Shinzaemon, coincidentally meets Toyoshiga, the daughter of Soetsu. They fall in love. It is a doomed love, as the spirit of Soetsu is far from dead.

Zebraman awakens 15 years in the future, unclear on what has happened to him, and quickly discovers that the evil Zebra Queen has a hold on Tokyo.