A man named Soichi Tsugami has lost his memories. He doesn't know who he is, where he came from, or how he came upon his peculiar circumstances. Tsugami, seemingly for no reason, transforms into a powerful superhuman, Agito, whenever in the presence of the beings referred by the police as the "Unknown", a race of powerful monsters that have been causing murders around Tokyo, targeting certain people as their prey. In response, the police department unleash their newest weapon: the G3 powersuit, originally developed to fight against the "Unidentified Lifeforms", the enemies of No.4 (Kamen Rider Kuuga). G3 and Agito don't know whether they should join up and defeat the Unknowns, their common enemy, or to combat each other, keeping the mysteries that entwine them separate. Ultimately, even more mysteries unfold, with the appearance of Kamen Rider Gills, who is on a search to uncover why his father committed suicide. These mysteries and others collide, as the true nature of Agito would ultimately determine the fate of humanity.

Hana Yayoi (Takajo Aki) is a descendant of special family which has super human knowledge, good at information war. She has keen powers of observation to see through people's secret, and her twin brother (cast by Former D-BOYS member Endo Yuya) has over 180 IQ.

Angkor is the beautiful daughter of a high rank officer of Cambodia. Before she was born, her father had slain a tiger. The spirit of the tiger lives on inside of Angkor and possesses her when she looses herself to her anger. An inner struggle in Cambodia forces Angkor and her friend/body guard, Koytee, to flee to Thailand. Along the way, they get separated. Angkor eventually arrives at the refugee camp in Thailand alone awaiting Koytee. There Angkor meets Pookong Kan, who was secretly sent to investigate the case of several missing and deadly war weapons that may be linked to a few of the officer's corruption. By chance, Angkor gets mixed up and becomes an important witness to the murder of Pookong Kan's comrades by Muad Rit.