A mysterious enemy known as Unknown suddenly appeared in the past. To counter this threat, the Evolutionary Railway Development Agency, also called ERDA, developed the Shinkalion, a robot that transforms from a bullet train. Taisei Onari, a second-year junior high school student, transfers to Shinkai Gakuen in search of clues about his older sister who disappeared two years ago. Shortly after his arrival, the Unknown resurfaces for the first time in a decade. It is then discovered that Taisei possesses an exceptionally high aptitude as a Shinkalion pilot, forcing him into the decision to fight.

The main cast of pilots includes Taisei, who operates the E5 Hayabusa unit, and his friends at the academy. Akane Folden, a cool and confident boy with a French father and Japanese mother, pilots the E6 Komachi but has stepped back from a promising athletic career due to injury. Ryota Kuzuryu, who admires the Shinkalion after being saved by one as a child, pilots the E7 Kagayaki and becomes Taisei’s first friend. Other key pilots include Ten Uotora, a genius first-year student known as the genius driver piloting the N700S Nozomi, and Shion Goryokaku, a quiet martial artist piloting the H5 Hayabusa. They are supported by Bina, a highly expressive navigation AI created by Taisei’s sister, and Mai Oume, a manager who aspires to be an engineer. ERDA staff include commander Kadomichi Takanawa, researcher Agano Tsugawa, and command center operators Sorachi Iwamizawa and Miyoshi Ochiai.

The story follows the boys growth and determination as they pilot their Shinkalion units to uncover the true identity and purpose of the Unknown, as well as the truth behind the disappearance of Taisei’s sister, Ina.