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.

In preparation for more Unknowns to appear, Taisei stays in Tsuruga and enjoys the railway museum he once visited with his sister.

Meanwhile, Ryota is training alone to raise his Aptitude Value.

Ryota has a strong admiration for the Shinkalions because a Shinkalion saved his life when he was young. Although he feels regretful that he was unable to protect Tsuruga with his own hands, he still hides his true feelings.