After the defeat of Myouri Unzen at the hands of Medaka Kurokami and her Student Council, peace has returned to Hakoniwa Academy—at least, for a short while. Soon, Medaka, Zenkichi Hitoyoshi, Kouki Akune, and Mogana Kikaijima find themselves wrapped up in another sinister scheme, known as the "Flask Plan," led by the school's principal himself.