Following Medaka Kurokami, a charismatic and attractive first-year Hakoniwa Academy student who is elected Student Council President with 98% of the vote. She institutes a suggestion box, and with the help of her childhood friend (You), addresses these requests in an unconventional manner. Over the course, she distributes the student council leadership positions to other students such as Kouki Akune and Mogana Kikaijima.

The Student Council learns that the academy chairman intends to initiate the Flask Plan, a project to forcefully experiment on regular students, called Normals, in order to turn them into humans with superhuman abilities called Abnormals. The Student Council infiltrates the academy's secret lab and battles other students that are involved with the project.

Shortly after, the Student Council are challenged to a tournament by Misogi Kumagawa who wishes to replace Medaka's Student Council with one of his own. After Kumagawa's defeat, two students are unsealed from his powers and complete their transfer to Hakoniwa Academy. The two are more powerful than Abnormals and are dubbed "Not Equals". Their leader, Anshin'in, threatens to restart the Flask Plan once Medaka graduates, forcing the Student Council to train their successors.

Name: Age: Appearance: Personality: Gender: Height: Occupation: Affiliation: Relatives: Education: Mentality: Abilities: Abnormality: Main Ability: Background: