At the renowned Shuchiin Academy, Miyuki Shirogane and Kaguya Shinomiya are the student body's top representatives. Ranked the top student in the nation and respected by peers and mentors alike, Miyuki serves as the student council president. Alongside him, the vice president Kaguya—eldest daughter of the wealthy Shinomiya family—excels in every field imaginable. They are the envy of the entire student body, regarded as the perfect couple. However, despite both having already developed feelings for the other, neither are willing to admit them. The first to confess loses, will be looked down upon, and will be considered the lesser. With their honor and pride at stake, Miyuki and Kaguya are both equally determined to be the one to emerge victorious on the battlefield of love!

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.

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.