In the franchise's story, Hayato Hayasugi, 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.
 
(Source: Anime News Network)

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A group called the Shinkansen Ultra Evolution Institute was investigating a recent rash of monster attacks happening in Japan after the appearance of a mysterious Black Shinkansen. The SUEI had a major weapon for the fight - Shinkalions, bullet trains that can transform into giant mecha. One boy, Hayato Hayasugi, was a huge fan of trains and stumbled upon his father’s secret work for the SUEI. Surprisingly, Hayato soon became a Shinkalion driver! As perhaps Japan’s best chance of survival, Hayato and other kids take on the great responsibility of fighting otherworldly enemies. 

Now, a new giant enemy has come from space looking to conquer the planet. Although the SUEI have a new prototype Shinkalion known as the ALFA-X to take up the fight, Hayato’s father, Hokuto, disappears. A 9-year-old version of Hokuto leaps through time to the present to help fight the alien attackers and drives the ALFA-X! 

(Source: Tokyo Otaku Mode)

Shinobu Tsukiyama