"Unknown" is a mysterious enemy that suddenly appeared a long time ago. As a countermeasure, the "Evolutionary Railway Development Agency" (ERDA) has developed the "Shinkalion" robot that transform into bullet trains, to prepare for the threat.

"I want to be a cool person who can protect something..." Taisei Oonari, a second-year junior high school student, transfers to Shinkai Gakuen Middle School in search of clues about his older sister who disappeared two years ago.

Just then, the Unknown appears for the first time in 10 years. Taisei happens to have a high aptitude value as a Shinkalion pilot, and is forced to make a decision to fight it. What is the true nature of the Unknown and what is its purpose? What is the truth that comes to light at the end of the fight? The story of the boys' determination and growth begins now.