In "Medaka Box," Kurokami Medaka, a first-year student, becomes Student Council President and creates a suggestion box called the "Medaka Box." She invites all students to share their concerns freely, promising to solve every single one.
After winning the Student Council election with 98 percent of the votes, Medaka, as the only council member, enlists her childhood friend Hitoyoshi Zenkichi, who reluctantly takes the lowest position in the council. The team grows when Medaka recruits Akune Kouki, a former judo club member, as secretary, and Kikaijima Mogana, a current swim club member, as treasurer, for a daily payment of 300 yen.
The Student Council works on solving problems reported through the Medaka Box, handling various challenges like students in the wrong clubs causing trouble, girls asking for advice on love letters, and people searching for lost pets. Through these efforts, they slowly earn the trust and respect of the entire school.