After the events of Ultraman Saga, Ultraman Zero goes to the Monster Graveyard to train with his new powers. There, Zero encounters Alien Bat Glacier; a follower of the original Bat that took over the alternate world. He revives the monster army, the Four Beast Warriors of Hell from the Graveyard to fight Zero for defeating his leader.

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.