After Myouri Unzen's defeat at the hands of Medaka Kurokami and her Student Council, peace has returned to Hakoniwa Academy—at least for the time being. Soon after, Medaka, Zenkichi Hitoyoshi, Kouki Akune, and Mogana Kikaijima become entangled in another evil plan known as the "Flask Plan," which is directed by the school's principal himself. The council's first concern, however, is dealing with a new gang of superhuman pupils known as the "Thirteen Party," led by the egocentric but strong Oudo Miyakonojou. With the mysterious Flask Plan, Oudo's dictatorship, and the reappearance of an old foe, the status of Hakoniwa Academy is far from calm, and Medaka and her comrades have their hands full as things only become crazier.