X, intending on using the strong destructive tendencies of humans, especially children, releases Kabutoron in the city. It destroys things using the children's brain waves.

The children are happy when they find big stag beetles in one of the open areas, something which rarely happens in town. Also Jinpei finds one of the bugs and brings it home.

In that night, each of the children's stag beetles grow large and they pull the children inside their bodies, fly out the room and start to destroy the city.

While flying, Ken discovers how Kabutoron attacks a nuclear plant. But since Jinpei is missing, the God Phoenix cannot take off.

Ken transmutes into his G1 plane and uses his X-ray on Kabutoron. Because he sees a child in the interior, he ceases to attack. The four members of the Science Ninja Team shadow Kabutoron and discover a base hidden in an ancient ruin.

In the interior of the base, an operation intending to remove the children's brain and install them into Kabutoron is about to begin. A drill is just touching Jinpei's head when he's saved by a hair's breadth by Ken and Jun. They save the other children with Joe's help. Ken and the others get into the God Phoenix. Bombed by Red Impulse, Kabutoron blows up together with the base.