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.

Yuuta Hibiki wakes up in the room of Rikka Takarada and notices two things: he has no memories, and he can hear a mysterious voice calling his name from a nearby room. On further inspection, he finds a robot—which introduces itself as Hyper Agent Gridman—behind the screen of an old computer. Much to Yuuta's surprise, Rikka cannot hear Gridman, nor can she see the ominous monsters looming over a thick fog as it envelopes the town outside. Another giant monster materializes in the city and proceeds to wreak havoc. Amidst the confusion, Yuuta is once again drawn to the old computer and merges with Gridman. Suddenly, he appears in the middle of the battle and is forced to fight the monster. Together with Rikka and fellow classmate Shou Utsumi, Yuuta forms the "Gridman Alliance" to defeat the monsters plaguing the city and find whoever is responsible for their emergence.