Takeshi Hongo is a promising young man with a passion for motorcycle racing. However, his dreams are suddenly ruined when he gets kidnapped by Shocker, the evil secret organization planning to dominate the world. After being remodeled into a cyborg, Takeshi escapes and swears to protect the world from the inhuman monsters.

An amnesiac, happy go lucky youth named Shoichi Tsugami uses the power of Agito to unravel his mysterious past and battle beings known as Unknowns. In response to the Unknown threat, the police unleashed their newest weapon, the G3 powersuit primarily used by Makoto Hikawa. More mysteries unfold with the appearance of Ryo Ashihara, who transforms into a pre-Agito known as Gills. He seeks the truth about his father's suicide. These mysteries and others collide, as the true nature of Agito would ultimately determine the fate of humanity.

Shouichi encounters a teenage girl called Sayaka, who ran away from a military facility because of an attack by the Ant Lords. Sayaka has a supernatural ability to foresee the future. Risa Fukami, of the military group GA, wants to use that power to enhance the newly-made G4 System, which was based upon designs stolen from Ozawa. Now, Agito and Gills must fight to stop the Ant Lords' attack, as G3 and G4 settle their score.