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Junki Saiga is a normal high school student with a gift in mathematics. His daily routine is disrupted when his family gets news that his father's remains have been discovered- a noted archaeologist and researcher who had gone missing while exploring a site many years before. Among his remains were notes and artifacts that needed to be identified by the family near a notable triangular mountain in Japan known as "Japan's pyramid", a place suspected by some to be man-made.

A meteor containing a strange robotic lifeform falls from the sky and begins to cause destruction, putting Junki in danger and causing a mysterious bracelet from his father's research to activate and merge him with an ancient robot buried within the pyramid- a robot the runes describe as Reideen. It is now up to Junki and guardian Reideen to fight against this unknown alien threat from the sky.

As the story progresses attacks come from multiple directions: the main aliens, who only want Reideen's power, and will then raze the Earth and move on; a faction within the Vigilance Corps (similar to Japan's Self Defense Force) that wishes to discredit and remove Reideen in favor of Human-built remote-controlled mecha; and Roxell, an alien with horns on his head who used a similar giant named Gadion on his homeworld, only to be defeated by the overseer aliens, and his planet destroyed. Some of these enemies want Reideen with or without Junki as its pilot/power source, while others just want Junki/Reideen out of the way.

Junki grows continually torn between doing what only he can do, in piloting Reideen against the giant beast machines sent to destroy cities and the landscape, and his enemies' attacks toward him while he does not receive any help from the Vigilance Corps nor his friends.