The anime film is set in the Gridman Universe that is originally created by Tsuburaya Productions, and features characters from SSSS.Gridman and SSSS.Dynazenon.

Yūta voluntarily fuses with Gridman again to fight the kaiju, and is assisted by the return of the Neon Genesis Junior High Students, who now count a newly revived Gauma who commands DynaRex as their newest member.

Gridman and the NGJHS defeat the kaiju, and explain that some unknown phenomenon is causing different universes to overlap in a potential Big Crunch.

The NGHJS decide to stick around to observe the situation in case more kaiju return, and Yūta starts to see what he believes are ghosts.

Akane frees Alexis Kerib from confinement and takes remote control of him, attacking the mastermind behind the assault on Gridman's mind, Mad Origin.

Mad Origin reveals he is an embodiment of chaos, the antithesis of Gridman who wants to steal his ability to create universes.

Gridman regains control of himself and summons the Dynazenon crew, the NGJHS, Knight, and the 2nd to battle Mad Origin and with everybody working together, they are able to defeat him thanks to Alexis Kerib's sacrifice.

Yūta, Rikka, and Utsumi rewrite their play, titled "Gridman Universe", which proves to be a huge success.