45 years ago, a man was subjected to the experiments of the secret organization Shocker and became a cyborg. Since that day, the man's sole mission has been protecting humanity and justice from the threat of Shocker. His name is Takeshi Hongo, the first Kamen Rider. After a long battle overseas, Hongo hears a certain girl is in danger and immediately returns to Japan. He then meets Takeru Tenkuji, Kamen Rider Ghost, who had been investigating the girl's whereabouts.

In the Edo period, at the remote village of Okitsu, the evil cult leader Koushirou uses ninjutsu to bewitch sharks and forces them to attack local pearl divers so the cult can steal the pearls from their mangled corpses. Desperate for help, the village chief hires Kotaro Shiozaki, a guard at a nearby temple, but Kotaro soon finds his path blocked by lady ninja Kikuma and a gigantic shark that doesn't seem like something from this world.