Taisei Onari, a railway-loving second-year junior high school student, transfers to Shinkai Academy in search of clues about his missing older sister, Ina.

Just when he meets Ryota Kuzuryu and Mai Ome, and is excited about the railway club they are affiliated to, Unknown emerges in the city for the first time in ten years.

Incidentally, Taisei is found possessing high Aptitude Value as a Shinkalion driver, and is forced to make the decision to fight.

Taisei rides Shinkalion E5 Hayabusa and goes into his first battle. Although he is forced to struggle with unfamiliar driving, he manages to Vehicle Combine under Takanawa's instructions and somehow succeeds in defeating the Unknown.

However, Taisei feels responsible for not being able to protect the pedestrian bridge where he and Ina watched the E5 series road transportation when they were young.