"Himitsu Kessha Yaruminati" centers around a group of high school students who form a secret society to combat a mysterious organization known as the "Yaruminati." The Yaruminati is a shadowy group that manipulates events and people behind the scenes, often causing chaos and misfortune. The protagonists, led by the determined and resourceful Haruto, discover the existence of this organization after a series of strange occurrences at their school. Each member of the group possesses unique skills and backgrounds, which they use to uncover the truth and thwart the Yaruminati's plans.

The narrative unfolds as the students delve deeper into the conspiracy, encountering various challenges and adversaries. They uncover that the Yaruminati has infiltrated multiple aspects of society, including their own school, and is orchestrating events to maintain control and power. The group must navigate a web of deceit, betrayal, and danger as they work to expose the organization and protect their friends and community.

Key characters include Haruto, the de facto leader with a strong sense of justice; Aoi, a tech-savvy member who provides crucial information and hacking skills; and Riku, a former delinquent with a knack for combat. Other members bring their own expertise and perspectives, contributing to the group's dynamic and effectiveness. As the story progresses, the students face moral dilemmas and personal struggles, testing their resolve and unity.

The plot is driven by a series of missions and confrontations, each revealing more about the Yaruminati's motives and methods. The students' efforts to dismantle the organization are met with escalating threats, leading to intense and suspenseful situations. The series balances action, mystery, and character development, creating a compelling narrative that keeps viewers engaged. Through their journey, the protagonists grow individually and as a team, ultimately striving to bring down the Yaruminati and restore order to their world.