It takes place in 2005 (initially referred to only as "the 21st Century"), two years following an incident where the first identified extraterrestrial intelligence—classified as "EI-01"—crash-landed on Earth and absorbed a large number of machines into itself before disappearing without a trace. Following this incident, the Japanese government created a secret organization to combat potential alien threats: the Gutsy Geoid Guard, or "GGG", based beneath G-Island City in Tokyo Bay. Parasitic alien life-forms known as "Zonderians" have begun to emerge; using the Zonder Metal of which they are made, they can assimilate various kinds of matter to form "Zonders." which use humanoid beings as their hosts.

GGG gains three key resources with which to combat this threat. There is Galeon, a sentient mechanical lion of alien design. There is the alien child Mamoru Amami, whom Galeon had left with human parents eight years earlier. The third asset is human cyborg Guy Shishiō, whose life was saved by Galeon two years earlier and is capable of fusing with him, forming the mechanoid GaiGar. When combined with the GGG-made GaoMachines, GaiGar becomes the Super Mechanoid GaoGaiGar: a mecha capable of defeating Zonders, recovering their cores for Mamoru to "purify" and saving the human host in doing so.