The manga is set in the year 2048 and centers around Hiryu, a young Super A-grade Strider who retired early during his career after he was forced to kill his elder sister Mariya, a Strider who went insane (as shown in the prequel story). The main series begins with Hiryu living peacefully in Mongolia when his former superior, Vice Director Matic, forces him out of retirement in order to kill his best friend Cain, who has been captured by hostiles in the Kazakh SSR and has become a liability to the rest of the Striders. With the help of Strider Sheena, Hiryu manages to rescue and extract Cain, but he attacks them after regaining consciousness. Hiryu manage to subdue Cain, but not before Sheena is mortally wounded and dies. Hiryu uncovers a small device implanted under Cain's neck and learns that he has been the subject of a mind-control weapon codenamed Zain and that Hiryu's sister Mariya was under the influence of Zain when she went rogue. After Cain regains his sense and freewill, he decides to make amends for Sheena's death by teaming up with Hiryu and stop the Zain project from reaching its completion. The two learn that an organization known simply as the "Enterprise" is behind the Zain project and that Matic himself was cooperating with the Enterprise leader Faceas Clay. With the help of Cain, Strider Chief Kuramoto, and a group of other Striders, Hiryu manages to thwart Matic and Clay, and destroy the main Zain terminal.