After Medaka Kurokami and her Student Council defeated Myouri Unzen, Hakoniwa Academy experienced a temporary period of tranquility. Unfortunately, the peace is short-lived and the group is thrust into a new ordeal known as the "Flask Plan," which was concocted by the school principal. However, their first obstacle is to confront a newly-formed superhuman student organization called the "Thirteen Party," led by the haughty and formidable Oudo Miyakonojou. With the progression of the Flask Plan, Oudo's dictatorship persists, and an ancient foe resurfaces, causing Hakoniwa Academy to remain in a state of unrest. Medaka and her comrades face daunting challenges that require their full focus and attention.