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…

One day after school, first-year high school student Yomogi Asanaka comes across a starving man under a bridge. Introducing himself as Gauma, the strange drifter informs Yomogi that he is a "kaiju user," a person who deals with the "kaiju"—monsters who bring harm to the city and its citizens. The following evening, Yomogi runs into Gauma and his classmate Yume Minami. Simultaneously, a kaiju appears in a populated area of the city. Due to Gauma's lack of experience controlling the kaiju, he brings out a mysterious object from a glowing pouch, summoning a giant robot known as Dynazenon. Requiring the cooperation of four people, the mecha drags Gauma, Yomogi, Minami, and Koyomi Yamanaka—an unemployed man who was wandering on the street—into its cockpit. Their encounter with the kaiju marks the beginning of their entanglement with kaiju eugenicists—kaiju users who manipulate kaiju with ill intent—and their efforts toward bringing out the full potential of Dynazenon.

In a not so distant future, humans can upload their individual consciousness to a sentient machine after they have died. This allows them one final day on earth to rebuild their memories through the eyes of a bionic vessel.