In space, Ultraman Cosmos is battling with Baltan to stop him from invading Earth. A young boy named Musashi (Kounosuke Tokai) who is a 5th grader has a lot of dreams, such as becoming an astronaut to sail the sea of stars, and to meet Ultraman. One night, Musashi went to the forest to observe an eclipse with his friends. Unfortunately, that night, a heavy rain fell that made everybody decide to go home except for Musashi. Meanwhile, in the middle of that rain, Ultraman Cosmos is battling with Baltan to stop him from invading the city. They both use their powers and clashed at each other. Due to the impact made by their power clash, both of them were thrown into different directions.

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!

It has been a year since Musashi retired from being a Team EYES member and now he is finally pursuing his dream of becoming an astronaut.