The storyline begins in the near future, as referenced from the mid-1960s (in episode 23, "My Home Is Earth," it is definitively established that the series takes place in the early 1990s, via a plaque shown at the end of the episode dated 1993). Sinister aliens and giant monsters constantly threaten civilization during this period. The only Earth organization equipped to handle these disasters is the Science Special Search Party, or SSSP, a special worldwide police force equipped with high-tech weapons and vehicles, as well as extensive scientific and engineering facilities; this organization is called the Science Patrol, or the United Nations Scientific Investigation Agency, in the English-dubbed version syndicated in the United States. The branch of the Science Patrol that is focused on in the series is located in Tokyo, Japan. Led by Captain "Cap" Toshio Muramatsu (shortened to "Captain Mura" in the dubbed English-language version), the Science Patrol is always ready to protect the Earth from rampaging monsters, but sometimes it finds itself outclassed. When the situation becomes desperate, Shin Hayata, the Patrol's most capable member, holds the key to salvation in the form of the "Beta Capsule," which, when activated, allows him to transform secretly into the super-humanoid-powered giant from space, who becomes known to the people of Earth as Ultraman.
Ultraman remains until the threat is neutralized and then flies away to revert back to Hayata (this was shown twice by Ultraman firing a ring of energy from his hands that would fly to safe location and then energy from it would materialize Hayata even as Ultraman fades away at the same time). Ultraman's victory is never assured however, as Ultraman's powers—his very life force—comes from rapidly depleted, stored solar energy. At the beginning of each transformation from Hayata-to-Ultraman, the "warning light" on the giant's chest begins as a steady blue color. Yet as Ultraman exerts himself, the "Color Timer," as it is also called, turns red, then blinks—slowly at first, then with increasing rapidity—as his energy reserves get closer to exhaustion. As the voice-over narration reminds the viewer, beginning with episode 2 and for each episode thereafter, if Ultraman ever reaches the point of total energy depletion, he "will never rise again."
In episode 39, "Farewell Ultraman," Ultraman fights an enemy called Zetton, leader of an army of monsters bent on destroying all the Ultra-Crusaders, who employs an unexpected weapon against Ultraman—one which damages his Color Timer/warning light and disables his ability to measure his power supply. As a result, Ultraman stays in his full-size form too long and collapses into a dormant state. Fortunately, despite this loss, the Science Patrol's members are able to defeat Zetton on their own. When Zoffy, Ultraman's superior, comes to retrieve the fallen hero, Ultraman pleads for Hayata's life and offers his life completely, so that Hayata may live as a normal man. Zoffy then says he has brought two life-forces and that he will give one to Hayata. He then separates them, giving Hayata new life, but Hayata seems to have no memory between the time he first collides with Ultraman's ship (in the first episode), and his standing outside Science Patrol Headquarters as he watches Zoffy take Ultraman home. This is a rather different finish to the series than stated in the English dub, which states both that Ultraman will return and that Hayata retains his beta capsule as he awaits Ultraman's return.