Upside-down rainbows are being sighted throughout Japan. They are said to herald the onset of rain. Gento suspects that a kaiju may be behind this and decides to visit Professor Yokomine, a leading kaijuologist and also his mentor from school. Yokomine tells him about Nijikagachi, a god-like being that can at times bless the land with rain and at times summon utter destruction. That's when Gento receives news about an appearance of a giant kaiju!

The typhoons that Nijikagachi created are about to wash away civilization. Gento decides to deploy Earth Garon's new Mod.2 unit into battle to defeat Nijikagachi. Teruaki, who had a deep respect for Yokomine, goes to persuade the mastermind of the plot.