"Tantei Gakuen Q" centers around a group of young students enrolled in the Dan Detective School (DDS), an institution founded by the legendary detective Morihiko Dan. The school trains aspiring detectives to solve complex cases and mysteries. The protagonist, Kyu Renjo, is a bright and curious boy with a natural talent for deduction, inspired by his admiration for Dan. He joins the school alongside his classmates: the intelligent and analytical Ryu Amakusa, the resourceful and tech-savvy Kazuma Narusawa, the kind-hearted and perceptive Megu Minami, and the enigmatic Kinta Himekawa, who possesses incredible physical strength.

The series is structured around episodic mysteries and overarching plotlines. The students, forming the Q Class, tackle a variety of cases ranging from seemingly simple puzzles to high-stakes criminal investigations. Their teamwork and individual skills are tested as they uncover hidden truths, often encountering dangerous adversaries. The cases often involve intricate clues, logical reasoning, and unexpected twists, showcasing the students' growth as detectives.

A significant subplot involves the mysterious organization Pluto, which serves as the primary antagonist. Pluto is a shadowy group of criminals with ties to the DDS, and their motives and operations become increasingly central to the narrative. The Q Class faces off against Pluto's agents, who are skilled in deception and manipulation, leading to intense confrontations and moral dilemmas. The conflict with Pluto gradually reveals deeper connections to the students' pasts, particularly Kyu's, whose father was a detective linked to the organization.

The characters' development is intertwined with the mysteries they solve. Kyu's determination and optimism drive the group forward, while Ryu's analytical mind provides critical insights. Megu's empathy and intuition often uncover emotional dimensions to the cases, and Kazuma's technical expertise proves invaluable. Kinta's strength and loyalty balance the team dynamic. Their mentor, Kyosuke Maki, a former detective and instructor at DDS, guides them while grappling with his own unresolved history tied to Pluto.

As the series progresses, the stakes escalate, culminating in a confrontation with Pluto that challenges the students' resolve and abilities. The narrative explores themes of justice, trust, and the ethical complexities of detective work, blending episodic storytelling with a cohesive overarching plot. The series balances lighthearted moments with darker, more suspenseful elements, creating a compelling mix of mystery and character-driven drama.