After Leader X is seemingly destroyed for good at the end of Gatchaman II, a fragment of him that survived grows and mutates into Z. With the head of the Egobossler family, Count Egobossler (and his two subordinates Mechandol and Kempler), Z is bent on destroying the Earth, and the Science Ninja Team, once more. In the wake of Anderson's death, Dr.Nambu has become the new head of the ISO, while the team is now confined to the Gallatown (aka G-Town) underwater base. Engineer Kamo is introduced, and after the New GodPhoenix is destroyed early on, the team receives the new Gatchaspartan as their mecha. The Gatchaspartan has a special mode as well, called Hypershoot, that can only be utilized by Ken (with his new Gatchafencer sword). As the series progresses, it is learned that the radiation exposure from constant use of the Hypershoot is slowly killing Ken, and that continued use would mean death. Meanwhile, Z plans to destroy the earth with an antimatter asteroid, codenamed Poison Apple.

A video blogger attempts to fake cryptid sightings to boost his views, but gets more than he bargained for when his crew is slaughtered by a real monster. Elsewhere, students find themselves preyed upon by a sandworm-like beast, initiating a desperate struggle for survival on their own school grounds. With more of these attacks from mysterious creatures occurring, researcher Sousuke Banba tasks himself with delving into the mystery. With nothing but the keyword Kagewani to lead him, he scours the sites of recent attacks in hopes of finding a lead to eradicating the creatures for good. However, Sousuke finds that these threats to humanity are even closer to home when the pharmaceutical company, Sarugaku, starts to encroach on his investigation.

Deep in the countryside, a man named Okina works as a bamboo cutter in a forest, chopping away at the hollow plants day after day. One day, he discovers a small baby inside a glowing shoot. He immediately takes her home, convinced that she is a princess sent to Earth as a divine blessing from heaven. Okina and his wife Ouna take it upon themselves to raise the infant as their own, watching over her as she quickly grows into an energetic young girl. Given the name Kaguya, she fits right in with the village she has come to call home, going on adventures with the other children and enjoying what youth has to offer. But when Okina finds a large fortune of gold and treasure in the forest, Kaguya's life is completely changed. Believing this to be yet another gift from heaven, he takes it upon himself to turn his daughter into a real princess using the wealth he has just obtained, relocating the family to a mansion in the capital. As she leaves her friends behind to enter into an unwanted life of royalty, Kaguya's origins and purpose slowly come to light.

After surviving the onslaught at Sarugaku headquarters, Sousuke Banba resumes his investigation of the Kagewani monster hybrids. Armed with the ability to harness the Kagewani's power, the researcher now has a means to eliminate the creatures. But despite the benefits of this skill, it has one major drawback: Sousuke now struggles to maintain his sanity, with the power threatening to consume his body. Soon, threats old and new begin to rear their heads, as the upper echelons of Sarugaku become active once again and an assassin with a personal vendetta sets her sights on Sousuke. Nevertheless, he resolutely forges ahead on his mission, determined to track down the origins of the Kagewani and eliminate their threat once and for all.