The kaiju, Deltandal, is demolishing the city as it flies through the skies at Mach 9. Because Earth Garon cannot keep up with Deltandal's speed, SKaRD is unable to catch it. Meanwhile Emi finds out confidential information on the GGF labeled "V99" about space kaiju such as Bazanga and Gebalga. It seems to be related to a certain experiment that was conducted in the past.

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?

Varallon reaches the moon, dropping bombs one after another. If this persists, it will alter the moon's orbit, leading to catastrophic consequences for Earth. Command directs SKaRD to deploy to the moon in the Earth Garon Mod.4 to eliminate Varallon. A desperate space battle unfolds.

Blazar and SKaRD face defeat in their battle against Varallon on the moon. Meanwhile, Emi is captured by Dobashi. In a dire turn of events, Varallon descends to Earth. Adding to the mystery, there's an appearance of a mysterious fleet of messengers. What will be the fate of SKaRD and Earth Garon's battle? What truth does Emi discover? Will Gento and Blazar be able to protect Earth?