In order to protect the peace and safety of Japan from the mysterious Giant Monstrous Beings, "Shinkansen Transformable Robot Shinkalions" were developed by the Shinkansen Ultra Evolution Institute. In preparation for the attack of new enemies, the Ultra Evolution Institute is developing a new type of robot called "Shinkalion Z" as well as new armed enhancement vehicles called "Zailiners" that transform from conventional trains to power up the "Shinkalion Z". The children who became the drivers of "Shinkalion Z" with a high Compatible rate will work together with the institute staff members to confront the giant monsters that reappeared The emergence of unknown enemies- And the encounter of two boys.