Upon being elected Student Council President, first-year student Kurokami Medaka introduces a suggestion box for students to share their concerns, which quickly earns the nickname "Medaka Box." Medaka proclaims that no issue is too small for her attention and requests that students submit their problems without hesitation.
Despite winning the council election by an overwhelming 98% vote, Medaka is the sole member of the council. She enlists the help of her childhood friend, Hitoyoshi Zenkichi, as the least ranking member of the council. Eventually, Medaka brings on two more members, former judo club member Akune Kouki as secretary, and swim club member Kikaijima Mogana as treasurer on loan for 300 yen a day.
Together, the members of the Student Council diligently work to address the problems presented in the Medaka Box. They handle a variety of issues, from handling disruptive club members to drafting love letters and searching for lost pets. Their dedication to helping those in need earns them the admiration and respect of the entire school.