Takuto Tsunashi washes ashore on the remote Southern Cross Isle and enrolls at the local high school, quickly befriending Wako Agemaki and her fiance Sugata Shindo. The island also hides giant mechanical Cybodies buried underground and a secretive order called the Glittering Crux Brigade, whose plans turn on Wako's role as a shrine maiden, and Takuto is soon pulled into their rituals and conflicts. This manga adapts the same story as the Star Driver: Kagayaki no Takuto TV anime.