When he returns to Earth to attend the wedding of his friend in Saipan, Musashi meets a beautiful girl named Shau who claims to come from the bottom of the sea. Just then, Monster Scorpis reappears in the sky above the island and Musashi faces the monster in order to protect the girl. What is the girl's true form? And what is the strange shadowy form that follows the monster Scorpis?

Once again, Musashi has encounter Ultraman Cosmos. Now Ultraman Cosmos has gained some new modes to defeat Scropis. Musashi has joined Team Sea to save the Blue Area. But there is mysterious evil monster, Sandros, who wants to destroy the Earth. Now it is up Musashi and Ultraman Cosmos to defeat Sandros and who’s the other Ultraman?