The storyline follows Medaka Kurokami, a magnetic and appealing first year Hakoniwa Academy pupil who's elected Student Council President with 98% of the vote. She addresses these petitions in her improper way, and with all the help with her childhood buddy Zenkichi Hitoyoshi, institutes a suggestion box. On the span of the narrative, the student council leadership places are distributed by her to other pupils like Mogana Kikaijima and Kouki Akune.
The Student Council learns that the academy chairman means to initiate a job to powerfully experimentation on routine pupils, the Flask Plan, called Normals, so that you can turn them into Abnormals, that's people with superhuman powers. The Student Council conflicts with other pupils which are involved using the job and infiltrates the secret laboratory of the school.
Soon after, Misogi Kumagawa who wishes to replace the Student Council with one of his own of Medaka challenges to a championship the Student Council. From his powers, two pupils are unsealed after the defeat of Kumagawa and complete their transport to Hakoniwa Academy. The 2 tend to be more strong than Abnormals and are dubbed "Not Equals". Their leader, Anshin'in, threatens to restart the Flask Plan once Medaka grads, driving their successors to be trained by the Student Council. Nevertheless, the accurate strategy of Anshin'in would be to have the standing as Student Council President of Zenkichi usurp Medaka. Zenkichi succeeds and does so on the pretense of enhancing the student life. He convinces Medaka to permit the Flask Plan for those people who are not unwilling.
Took over from her responsibilities as president of the Student Council, Medaka shortly becomes involved in a championship to determine her husband. Medaka becomes the winner, choosing to wed Zenkichi after they both grad and enters herself. Shortly after, the close pal Hansode Shiranui of Zenkichi leaves the school. Zenkichi and medaka find she's to end up being another host for Iihiko Shishime, a 5000-year old being. He is defeated by medaka and vanishes after quitting the moon from crashing towards the Earth, simply to reappear in time for the year end service. Following her return, assume her dad's position ahead of her family's company conglomerate, the Kurokami Group, only to later return as the new chairwoman and Medaka determines to leave the academy. Ten years after, Zenkichi, had worked his way up the Kurokami Group, becoming a high level worker before reuniting with her, with both swearing to never get split again.