Hayato Hayasugi (his last name is a pun on the words for "too fast") and other children will serve as conductors to pilot the Shinkalion. The Shinkalion robots are various models of real-life Japanese bullet trains (shinkansen) that transform into robots to fight an unknown evil to protect the safety and peace of Japan. 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.

The new enemies, Nahane and Ohanefu, along with the mysterious new Giant Monstrous Beings appear from space to take over the Earth! Holding the key to these events is Shinkalion ALFA-X, which was secretly developed by the Ultra Evolution Institute...!? For Hayato and Team Shinkalion, who had been living in peace, the battle begins again.