Super Atragon begins at the end of World War II aboard the experimental Japanese submarine Ra. Produced with alien technologies provided by a strange woman named Annette, the Ra could have single-handedly decided the course of the war. But on its maiden voyage, it encounters an American submarine built with the same technologies, provided by Annette's counterpart, Avatar. The two submarines engage and are both sunk into the ocean.

The story moves to the present day, where large, black, cylindrical monoliths are emerging from the polar ice caps. Conventional weapons are ineffective against the cylinders, which appear to be part of a plan to destroy all life on Earth. Coming to the rescue is the Ra, which has been secretly repaired and is the only force on the planet capable of stopping the monoliths.

Super Atragon is based on the novel Kaitei Gunkan (Underwater Battleship), by Shunro Ohshikawa. An entertaining aspect of Super Atragon is the combination of advanced alien technologies with old Earth technologies like in Space Battleship Yamato and Kishin Heidan. Like in these other anime, the mix in Super Atragon gives a sense of nostalgia to old war films, while still providing a futuristic touch.

The Japanese name of Super Atragon is Shin Kaitei Gunkan (New Underwater Battleship). Given that the name of the battleship is Ra, one might wonder where A.D.Vision got the name Super Atragon. The likely source is a live-action Japanese film called Atragon, which apparently gave some inspiration to the anime.