The stage is the "Blue World" which symbolizes rationality, but it is being attacked and invaded by Nightfly O'Note, a life form from the "Red World" dominated by instinct. The 17-year-old protagonist Akira Asagi works as a researcher in the Blue World. Later, because of her outstanding ability, she is promoted to the frontline combat commander and is ordered to be in charge of the counter-ministerial defense agency across Ishigaki Island and Iriomote Island, commonly known as "Ryukyu LAG". There she met the students of the Sixth Combat Unit "IS", which was established four years ago after the Fifth Combat Unit was completely destroyed in a fierce battle. As an instructor, the protagonist leads six riders (Riders), also known as "Scared Rider Xechs", to fight bloody battles together to deal with attacks and threats from another world. In such a life, their friendship is gradually deepening.