"Zetsumetsu Kigu Shōjo Amazing Twins" centers around two sisters, Iyo and Ui, who are part of a secret organization tasked with protecting humanity from extinction-level threats. The series is set in a world where mysterious entities known as "Kigu" emerge, posing catastrophic dangers to humanity. These Kigu are remnants of ancient civilizations or forgotten technologies that have resurfaced, often with destructive capabilities. The sisters, equipped with advanced combat suits and weapons, are deployed to neutralize these threats.

Iyo, the older sister, is pragmatic and disciplined, often taking a leadership role in their missions. Ui, the younger sister, is more impulsive and emotional, contrasting with Iyo's calculated approach. Their dynamic is central to the narrative, as their differing personalities and approaches to combat create both tension and synergy. The sisters' bond is tested repeatedly as they face increasingly dangerous Kigu, each encounter revealing more about the origins and nature of these entities.

The plot unfolds through a series of episodic missions, each focusing on a specific Kigu threat. These missions are interconnected by an overarching mystery surrounding the true nature of the Kigu and the organization the sisters serve. As the series progresses, hints about the organization's hidden agenda and the sisters' own past come to light, adding layers of intrigue to the story. The narrative explores themes of survival, sacrifice, and the ethical implications of wielding power to protect humanity.

Supporting characters include members of the organization, such as scientists and strategists, who provide intelligence and logistical support for the sisters' missions. Antagonists range from rogue Kigu to rival factions seeking to exploit the ancient technologies for their own purposes. The series balances action-packed sequences with moments of introspection, delving into the psychological toll of the sisters' responsibilities and the moral dilemmas they face.

The story builds toward a climactic confrontation with a particularly formidable Kigu, which forces the sisters to confront their deepest fears and question their purpose. The resolution ties together the series' central mysteries while leaving room for further exploration of the world and its characters. "Zetsumetsu Kigu Shōjo Amazing Twins" combines high-stakes action with a thoughtful examination of its characters' inner struggles, creating a compelling narrative within a richly imagined setting.