故事发生在箱庭学园,黑神目泷(丰崎爱生 配音)是学园一年级的新生,作为学校里的学生会长,黑神拥有完美的外表,优异的成绩,强健的身体和丰厚的家底,如此完美的女神,在生机勃勃的校园里会遇见怎样有趣的故事呢? 人吉善吉(小野友树 配音)是黑神的青梅竹马,两人从小玩到大,彼此之间感情十分要好。作为支持率百分之九十八的学生会长,黑神联手人吉善吉设置了“意见箱”,同好友阿久根高贵(浪川大辅 配音)、喜界岛枫夏(芽野爱衣 配音)等人一起,解决校园中的各类疑难杂症。然而,随着黑神的势力越来越大,一些不友好的声音随之而来。Elected as student council president with 98% of votes, Medaka is a brilliant students who will help students any way she can. This leads to the introduction of a suggestions box, which will later be given the nickname of 'Medaka Box'. Some of the suggestions therein, however, will provide some tough challenges for her and her student council friends.