Three months ago, the kaiju, Leviera, appeared out of nowhere. The only way to deal with it was to temporarily drive it away with a new disinfectant, FK1, developed by the major chemical company Novaio.

There is a strange link between this mysterious kaiju and Novaio...

In order to find out the truth, Emi goes undercover to work under Sonezaki, the CEO of Novaio!

Practice runs for the new railgun, Mega Shot, are conducted in Anri's hometown. That's where Anri has an unexpected reunion with her childhood friend, Mizuho.

Mizuho begs for them to cancel the practice runs. She insists that the removal of the shrine for the installation of the Mega Shot will awaken Dorgo, the local guardian god, but Anri finds it hard to believe.

However, during the practice there's a big earth tremor...

Yasunobu was rambling about his day to Cururu, a washer at the laundromat, when Alien Cannan Herbie suddenly appears before him. Herbie uses the Aurora Beam to manipulate machines and this was the reason for the increasing car and airplane accidents around the world. And that's not the end of it: it turns out that Earth Garon had also been shot with the Aurora Beam! What will Yasunobu do?

Everyone who looked into the big hole went into a state of confusion. During the investigation, even Teruaki, Anri, and Yasunobu fall victim to this strange phenomenon. Emi boards the Earth Garon alone and will challenge the kaiju, Mogusion, with help from the voice interactive AI system, EGOISS.

Kaiju that have been defeated already start making a reappearance. However, they can walk right through people and obstacles. Everytime this occurs, a mysterious man with a big sword shows up and defeats the kaiju. Gento in an attempt to solve the mystery, tries to get ahead of the man by showing up at the next anticipated point of kaiju reappearance. There, he meets the mysterious man, Zangill, who supposedly wanted to speak with Gento. Zangill then reveals a secret about himself...

The kaiju, Irugo, breaks through the ground and surfaces. The gases exhaled from its mouth are poisoning the human body. SKaRD is ordered by CP to halt all investigation on Irugo and to standby until further orders. Emi thinks this could be the Third Wave, so she proceeds with her investigation involving the Test Facility 66. Meanwhile, the GGF sets out on a mission to cut off Irugo with a self-propelled laser cannon.

Multiple Irugos, which were thought to have been defeated, re-surface once again. As the GGF continues to investigate, a kaiju larger than Earth Garon emerges. Emi comes into contact with her father's former teammate, Nishizaki. Nishizaki reveils the truth about the explosion from three years ago, before Emi heads down to the Test Facility 66 alone. What will she find out?