After vanquishing Myouri Unzen, tranquility settles momentarily in Hakoniwa Academy. Yet, a fresh storm looms as Medaka Kurokami and her Student Council face the devious 'Flask Plan' orchestrated by the school's principal. Their first challenge arises from the formidable 'Thirteen Party,' led by the arrogant Oudo Miyakonojou. Amidst this chaos, old foes resurface, plunging the academy into turmoil. With the enigmatic Flask Plan, Oudo's oppressive rule, and looming threats, Hakoniwa Academy remains far from peaceful. As abnormality escalates, Medaka and her comrades must navigate this turbulent new reality.