Medaka Kurokami, the recently elected Student Council President of Hakoniwa Academy, has instituted a suggestion box in order to collect suggestions and improvements from fellow academy students. Together with Zenkichi Hitoyoshi, she solves problems, from finding lost dogs to cleaning up club buildings and even fixing personalities. During the course of the series, Kouki Akune and Mogana Kikaijima are recruited to the student council to help improve the school.
Soon, the Student Council discovers the existence of the Flask Plan, supervised by the Hakoniwa principal in order to experiment on students with supernatural abilities, dubbed as "Abnormals". The goal of the project is to find a way to mass produce Abnormal beings. However, once a method is found, the students of Hakoniwa Academy will be forced to endure the vicious trial which will result in the death of most of the students. After battling many foes, the Student Council are able to put an end to the Flask project. Their success is short-lived, with the immediate introduction of Misogi Kumagawa, a teenage boy with a powerful abnormality who plans on destroying the world. Using a school rule, he threatens to usurp Medaka's student council with one of his own, by defeating her council in battle.
After the defeat of Misogi, two students who were sealed by Misogi's ability are able to complete their transfer to Hakoniwa Academy. The two students contain multiple Abnormal powers and are called "Not-Equals". They are intent on reviving the Flask project once Medaka graduates. Medaka and her student council, now with Misogi in its rankings, attempt to stop the project's revival by training 5 students to be their successors; however the five are secretly aligned with the Not-Equals.
Information Source: Wikipedia