由少女．新条茜所创造的世界一度是「怪兽」肆虐之地，经过「Gridman同盟」的一番努力，成功开解少女封闭的内心，世界才恢复和平，不致毁灭。 危机结束一年后，响裕太决定向六花告白，谁知怪兽突然来袭，再次打破他们的日常。而Gridman亦再度回归，告知裕太「世界的平衡正在崩坍」。随着真红之强龙Dyna Rex、Gridman的支援者「新世纪中学生」，甚至异世界的居民陆续出现。谜样的敌人藏于暗处，「世界崩塌」的真相未明，Gridman同盟应如何应战？裕太珍藏已久的感情又能否成功传达？

在都立杜鹃台高中放学后的教室里，响裕太反复在笔记本上画着又擦去那个应该存在于他记忆中的GRIDMAN。这个世界曾经被一名少女创造并破坏，最后是来自异次元的电光超人GRIDMAN，和那名少女制造出来拥有心的怪兽，以及裕太一行人，拯救了那名少女的心。

升上高中二年级后，裕太决定向分发到不同班级的六花（宫本侑芽 配音）告白。然而，和平的世界与日常生活却随着轰隆巨响开始崩坏。就在裕太等人面临危机之时，GRIDMAN突然现身，并说道“这个世界的平衡即将瓦解。”。

不久，深红的强龙DYNAREX、GRIDMAN的助手‧新世纪中学生，以及来自另一个世界的麻中蓬等人出现在裕太面前。

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.

22 years ago… A boy, Takeshi Todo, who attempted to take over the world with the devil of the Computer World together. He reformed himself after the battle and now needs the power of the Hyper Agent. Again, the evil is going to appear in the real world. A materialized monster is now approaching! Enter the battle code! The access code is… “GRIDMAN.”