"Xtra Credit" centers on a group of high school students navigating the pressures of academic life while uncovering a mysterious system that allows them to earn extra credit through unconventional means. The protagonist, Haruto Saito, is a reserved yet determined student struggling to maintain his grades while balancing part-time work and family responsibilities. After discovering a hidden app on his school-issued tablet, Haruto is drawn into a series of challenges that test not only his academic knowledge but also his moral compass and interpersonal skills.

The app, known as "Xtra Credit," presents tasks that range from solving complex puzzles to completing real-world missions, often blurring the lines between right and wrong. Haruto is joined by a diverse group of classmates, each with their own motivations for participating. Aoi Takahashi, a top-performing student, seeks to prove her intellectual superiority, while Riku Nakamura, a rebellious underachiever, sees the system as a shortcut to success. Yuna Matsuda, a quiet but observant classmate, becomes Haruto's closest ally, offering emotional support and strategic insight as the challenges grow increasingly perilous.

As the group progresses, they uncover the app's origins, tied to a shadowy organization experimenting with gamified education to manipulate student behavior. The stakes escalate when the tasks begin to impact their personal lives, forcing them to confront ethical dilemmas and the consequences of their choices. The narrative explores themes of ambition, trust, and the societal pressures placed on students, while maintaining a focus on the characters' growth and relationships.

The story builds toward a climactic confrontation with the organization behind "Xtra Credit," as Haruto and his friends must decide whether to dismantle the system or use it to their advantage. The series balances its suspenseful plot with moments of camaraderie and introspection, creating a compelling exploration of the challenges faced by modern students.