In the franchise's story, Hayato Hayasugi (his last name is a pun on the words for "too fast"), the train-loving son of a train museum curator, accidentally stumbles into his dad's secret research lab one day. Inside he finds the E5 bullet train. As soon as he enters, he hears an announcement that a mysterious enemy, the Bachigami ("bee god"), is attacking the city of New Saitama. Luckily, with the touch of his father's Shinca ("evolve") card, the bullet train he's in transforms into a mighty robot — the Shinkalion E5 Hayabusa.
In the anime's story, Hayato and other children will serve as conductors to pilot the Shinkalion. The children must work together with the adults of the "Shinkansen Ultra Evolution Institute" (SUEI) to defeat a monster that looks like a jet black bullet train.