Taking place 2 years after the events of Kamen Rider Kuuga, a young man named Shouichi Tsugami has no memory of his past or the events that lead to his memory loss. At the same time, creatures called the Lords (thought to be the "Unknowns" that Kuuga battled) have been targeting certain people for no real reason. Shouichi, for no reason, transforms into Kamen Rider Agito to defeat the Lords and to unravel the mystery to his abilities and his past.