As soon as Kiyotaka Ayanokouji and the rest of Class D officially enter their second year at Tokyo Metropolitan Advanced Nurturing High School, they face their next special test: each second-year student will have to team up with a first-year student to take a written exam. Although the test seems simple enough, every pair must achieve a specific number of points to avoid a harsh penalty, raising the demand for academically proficient individuals.

Without a break, Class D scouts for potential partners. However, Ayanokouji also faces a serious threat since the secret first-rate institution called White Room has enrolled another prodigy at the school to get him expelled. As Ayanokouji begins his masterful schemes once more, he must stay vigilant for new and old enemies alike.