She institutes a suggestion box, and with the help of her childhood friend Zenkichi Hitoyoshi, addresses these requests in an unconventional manner.

Their leader, Anshin'in, threatens to restart the Flask Plan once Medaka graduates, forcing the Student Council to train their successors.

Ten years later, Zenkichi has worked his way up the Kurokami Group, becoming a high-level employee before reuniting with her, with both promising to get married after another fight.

[18] Three light novel works, also written by Nisio Isin and illustrated by Akira Akatsuki, have been released by Shueisha under their Jump J-Books imprint.

A two-volume spin-off light novel series, titled Shōsetsu-ban Medaka Box (小説版めだかボックス), was released on May 2 and June 4, 2012.

[19][20] A second two-volume spin-off novel series, titled Medaka Box Gaiden: Good Loser Kumagawa (めだかボックス外伝 グッドルーザー球磨川), was released on October 10 and November 19, 2012.

[21][22] A prequel light novel, titled Medaka Box: Juvenile – Shousetsu-ban (めだかボックス ジュブナイル 小説版), was released on October 4, 2013.