A suggestion box: if you have a problem at school and want someone to help, you add it in the box. Simple, right? Student Council President Medaka Kurokami is about to learn that in her school, things don't go that smoothly. A new entry into the box reveals an unbelievable secret, one that threatens to engulf Medaka and Hakoniwa Academy into it's growing maelstrom. Along with her council members and their strange new found abilities, plus a big problem only they can solve, they're in for a wild ride, because a slip of paper can mean a world of trouble in Medaka Box!
Despite being a first year student, Kurokami Medaka has ascended to student council president. One of her promises is to institute a suggestion box. First suggestion? Defeat the delinquents!
Ariake-Senpai has a request: identify the culprit who has been giving her grief on the fiercely competitive track team. The student council, with the help of Shiranui, moves to take action.
After constantly visiting other groups' meetings, Zenkichi is quickly dubbed the "Club Crasher". Judo club is up next, but a request from the Judo club captain means the it's up to Medaka to stop him.
Zenkichi is down to his last point: if he loses this one, he has to call it quits. Meanwhile, Medaka sends the newest student council member on their first suggestion box assignment.
With more clubs than money, Sandbox Academy is about to get into a situation that will be hard to dig itself out of. A suggestion is made to hold an event at the new indoor pool.
The swim team is overpowering everyone at the Aqua Club meet, using any means necessary. Medaka notices this, and what happens next will shock everyone!
Things get awkward when another council member walks in on Kikajima while she’s changing. Medaka is called upon to model for Tabaru’s art piece. As always, things become complicated.
The Student Council’s rule bending has gone too far, and they find themselves under the surveillance of the Disciplinary Committee. Onigase—better known as the American Handcuff—makes it her duty to correct the council’s errors.
The leader of the Disciplinary Committee favors using excessive violence to solve problems. His newest problem is the student council!
Medaka successfully saves her classmates, and everyone escapes unscathed. Unzen's violent rage increases along with his desire to destroy the student council. His next encounter with Medaka will be explosive if he has anything to do with it.
Medaka's rage has erupted. The other Student Council members try to control Medaka's overflowing anger as she makes a decision to either save Unzen or destroy him.
The student council must persevere, even without Medaka.