Musashi is a 10 year old boy with big dreams. He wants to grow up to be an astronaut so he can fly through the stars and meet his hero Ultraman. His mother worries that Musashi daydreams too much, but his police officer father thinks a little bit of daydreaming never hurts anyone.

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?

An alternate version of Ultraman Cosmos 2: The Blue Planet, which was created due to the arrest of the film's star, Taiyo Sugiura. New scenes were filmed that are primarily set in the past. Musashi Haruno, now a middle school student, continues to pursue his dream to become an astronaut, which is also a promise he made with Cosmos. However, he is on the verge of despair because space development gets canceled due to a rocket accident. A mysterious girl named Shau appears in front of Musashi. She invites him to a mysterious parallel space and shows him a vision of what will happen to him 10 years from now. He witnessed a crisis of Earth's destruction caused by Sandros, the worst destroyer in the universe!