In the distant future, another world, S-1, has been badly polluted. Just as scientists find a way to clean up the planet, the followers of military fanatic, Zeo Gattler, invade his laboratory and destroy his work. The scientist's son, Marin, escapes and is angered over what his people have done but before he can do anything, he gets caught in a time warp and ends up near Earth in the year 2100. When Gattler's Aldebaren Army appears after destroying a Martian colony, Marin finds himself joining the military organization, Blue Fixer, which uses his ship as part of their recently completed robot, Baldios. Together, Marin and the Blue Fixer team face off against Gattler and the S-1 forces which are poised to take over the Earth and make it their new home.

During the final conflict with the Aldebaren Army, Gattler manages to trigger a massive tsunami which effectively destroys the surface of the Earth, leaving the Blue Fixer team helpless and unable to stop it. Marin can only watch in horror as wave after wave destroy the surface until a shot of the wave freezes and we are left with a caption saying "End". The last two episodes in the series deal with the Fixer Team's family and loved ones being destroyed by the natural disasters with the climax involving them removing the highly radioactive core of one of Gattler's submarines that threatens to cause radioactive contamination across the planet. The ending involved the unstable core exploding after being transported near Gattler's fleet, killing him and his troops. However, the Baldios movie which came out afterwards gave a slightly more fulfilling conclusion with Marin and Gattler getting a proper final confrontation and the fate of the Earth turning out to be not as abrupt.

In both the TV series and the movie it is disclosed that S-1 and the Earth are actually the same planet, the massive dimensional travel of S-1 troops being, in fact, a time travel and that the environmental catastrophe that's actually destroying S1 is the lasting effect of Gattler's Artificial Sun.