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.

Hayato cannot hide his anxiety after his father Hokuto goes missing during an enemy attack. Meanwhile, a 9-year old Hokuto suddenly appears from across time and space! The young Hokuto, who has slipped through time with the Glowing Particles, determines to become the driver of Shinkalion ALFA-X, which brings together the latest technologies to protect the Earth and return it to normal. Together in their thoughts, Team Shinkalion, brought together from Hokkaido Branch, Yamagata Branch, Ōmiya Branch, Nagoya Branch, Kyoto Branch, and Moji Branch confront the strongest enemy in the universe.

Can Team Shinkalion protect the peace and security of Japan!? Can Hayato reunite with Hokuto!?