Sometime ago, this world was created by a girl, and was then destroyed by her in order to vent her frustration towards the reality. It was Gridman the Hyper Agent, the humane monster she created, Yuta Hibiki and his friends who saved her heart. Yuta Hibiki had just become a second-year high school student and decided to reveal his feelings to his classmate, Rikka. However, Kaiju suddenly appeared and began to attack the city. Gridman came back from the alternate dimension and told Yuta that worlds of different dimensions which were once in harmony were rapidly losing their balance. When the red dragon Dyan Rex, the Gridman's supporters named “Neon Genesis Junior High Students”, and the residents of an alternative world, Yomogi Asanaka and his friends appeared one by one, Yuta was once again caught up in a great crisis…