Five youths from Edo City explore a strange rocky island and discover the mecha that Doctor Hoarai had been creating in order to resist the impending attack by a race of subterranean rock people.

Doctor Hoarai was ridiculed by the scientific community for his predictions that such an attack would take place. The youths decide to join the doctor (who was dead but had transferred his mind into a computer) in piloting the vehicles and protecting Earth. The Gowapper 5 Gordam team is born! With the aid of the giant fighting robot Gordam, the Gowapper team under the leadership of Youko Misaki must face the hordes of the inhuman subterranean people.

Gowapper was the first super robot anime to feature a female as the leader and main character. The concept of a group of young adults gathering to fight evil can be seen in other Tatsunoko works such as Science Ninja Team Gatchaman and in manga written by Tatsuo Yoshida and Ippei Kuri, but as of 2008, the only other Tatsunoko production featuring a female lead is Time Bokan 2000: Kaitou Kiramekiman. Gowappa 5 Gordam has a bright theme song and light-hearted situations, but the story also includes more serious parts, and there are episodes that end on a rather bitter note.