Star Blazers consists of three television seasons. Each is an English-language adaption of its Japanese counterpart Space Battleship Yamato. However, the Japanese saga entails more than just these three television seasons, and part of this missing portion of the saga occurs between Seasons Two and Three, in the movies Yamato: The New Voyage and Be Forever Yamato.

In the first season, Earth is attacked by Gamilon, a distant planet. The radiation from Gamilon's planet bombs forces everyone on Earth underground. With no way to remove the radiation, all life on Earth will be wiped out in one year. The Earth then receives unexpected help from Queen Starsha of the planet Iscandar, who offers a device called "Cosmo DNA" which will remove the radiation. However, since Iscandar is 148,000 light years away, Starsha also sends plans for the experimental Wave Motion Engine that, when constructed, will help whoever can travel to Iscandar by letting them travel at 27,569,736,000 miles per second (about 92 times the speed of light). On Earth, a crew is recruited, headed by Captain Avatar, and an old sunken battleship (the Yamato) is transformed into a spaceship (the Argo), outfitted with the Wave Motion Engine, and sent to Iscandar.

The second season takes place one year after the Argo returns to Earth with the Cosmo DNA and Earth's ecosystem is restored. It now faces a new, dangerous enemy, the Comet Empire, led by Prince Zordar. Unlike Gamilon, which was seeking to capture and colonize Earth, Zordar simply wants to conquer and annex Earth to his Empire. Desslok, the Gamilon leader, also joins forces with Zordar, mainly because he wants revenge on the Argo for having destroyed Gamilon. The series revolves around the Argo, now commanded by Deputy Captain Derek Wildstar, working with the Earth Defense Force to face Zordar.

In the third season, the Argo is caught in the middle of a war between the Galmans (the reformed Gamilon Empire) and the Bolar Federation. A stray missile fired during the war causes the sun's thermonuclear reactions to go out of control. Unless it can be stopped, the sun will destroy the Earth in one year and the entire solar system in three. Now officially in command of the Argo, Derek Wildstar is charged to help find a new home for Earth's population.