SKaRD finally welcomes the last member, Yasunobu, who had been involved with the development of the new weapon, Earth Garon. Now with the whole team gathered, they begin to train against kaiju. In the midst of this, they are informed of a mysterious phenomenon occuring around the world. Storage tanks with new energy sources are being emptied over night... SKaRD believes that this is caused by a kaiju and deploys Earth Garon to the field for the first time.

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?

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.

Anri receives a letter. It contained a concert ticket for a band led by Hoichi Tsukushi, someone that Anri had gotten to know through music. That's when the robot kaiju Garamon appears from a meteorite that came from outer space. Anri realizes that Garamon's behavior is controlled by a mysterious sound wave, and she has a hunch...

Gento's son, Jun, wants to go see a newly discovered egg shown on television, so the Hiruma family decide to go on a day trip to visit it. There, they witness the birth of Baby Demaaga. In the midst of the capture operation led by the GGF, the mother Demaaga makes an appearance. The GGF launches attacks as the parent kaiju approaches its baby. While evacuating, Gento can't help but feel mixed emotions seeing Demaaga trying to protect its child. Suddenly, the Blazar Brace appears on Gento's left arm.

Following the battle with Demaaga, Gento can not hide his confusion about the alien being that resides in his own body. That's when a meteorite flies in from outer space. It lands on Earth, evading the GGF's attempts to intercept it, and transforms into the kaiju Gebalga. It seemed that Earth Garon would have the upper hand in the fight until Gebalga revealed it's surprising ability...

As the network contamination by Gebalga continues to spread, SKaRD plans a new operation. Gento is distrustful of Blazar, who has once again acted against his will in the battle against Gebalga. He decides to leave the Blazar Stone in his locker. SKaRD decides to commence a major joint-operation by combining forces with the development team and the special forces unit.

Anri stays behind at SKaRD CP to compile the records of the battles they had fought so far. Yasunobu and Emi join Anri as she reminisces about the various battles. They eventually start discussing about a certain commonality between the space kaiju... Meanwhile, Teruaki asks Gento what he thinks about Blazar and...

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.

Gento's son, Jun is classmates with an unusual character, Arata. One day, Arata half-forcefully brings Jun to his secret base filled with his drawings of kaiju. Jun is moved by Arata's passion behind the drawings and his free-spirited soul. Jun draws a kaiju of his own and named it Gavadon. When night falls, a mysterious ray of light transcends down to the secret base and the drawing of Gavadon begins to beat like a heart.

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?

Teruaki rushes back to his parents' home when he hears that his father has fallen ill. However, this turns out to be a lie just to get Teruaki back home. Teruaki's father wants Teruaki to quit the GGF and the divide between him and Teruaki grows further. This is when they hear strange chirping from insects. Apparently, the quality of the soil in the fields has changed over the past month and the crops are dying. As Teruaki and his father go around, they find a strange cave in the mountains...

The fifth flight test of the Earth Garon Mod. 3 begins with Yasunobu as the pilot and Anri in the commander's seat. They reach the maximum speed of Mach 9 during aerial combat maneuvering. However, Yasunobu is unable to withstand the gravitational acceleration and loses consciousness. Because of this, he is discharged as the pilot of Mod. 3. In the meantime, a gigantic Deltandal appears, and Anri and Earthy are forced to pilot Earth Garon.

Tetsuo is a humble businessman working for the Japan Kaiju Damage Insurance Company. He doesn't have big goals and just drifts through life. However, he starts realizing the meaning of life through his interactions with Michiko, a homeowner he pitches a sales to. Meanwhile, Red King and Guigass appear, tearing through the mountains of the Alps. Tetsuo runs back for Michiko, who lives in the town where the kaiju are rampaging...

SKaRD is forced to deal with the appearance of kaiju around the world. Gento transforms into Blazar to fight them off as well, but the battles are taking a severe toll on his body. Earth Garon is dispatched to deal with Taganular's emergence in Koarai. However, at the same time, Taganular also appears in Nevada, US. Blazar is left with no choice, but to head down to fight it. However, that's when he discovers Taganular's surprising ecology.

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?