Kurokami Medaka is an exceptional first year student at Hanokiwa Academy who got elected as president of the student council with a smashing 98% of the votes. Extremely intelligent, strong, and rich; she wants to help anyone in need. To do that, she introduces a suggestion box that allows any student to contact her. Later known as the Medaka Box, it will bring forth incredible challenges to Kurokami and her friends of the student council.

The stage is set in "another Japan" as a banquet of diverse superhumans unfolds... In an imaginary "age of gods" about 20 years after the war, Japan has grown and developed by leaps and bounds. What if all the superhumans ever written about in fictional stories existed at the same time? Superhumans who came into existence through different circumstances, and who are special in different ways—Titans from outer space, lifeforms from a mystical world, phantoms and goblins from ancient times, cyborgs created by scientists, relics that rose out of the ruins of ancient civilizations, and the list goes on. One segment of these superhumans makes no secret of their existence and has gained popularity in society. Others cloak their identities and fight in secrecy. There are enemies of superhumans as well, organizations that operate in the shadows. The Japanese government has taken many measures to secure peace and order. One is the establishment of an organization under the Ministry of Health and Welfare—the Overpopulation Research Laboratory, a.k.a. the Superhuman Bureau. Their mission is to identify and approach superhumans, then oversee and safeguard them. One member of the Superhuman Bureau, Jirou Hitoyoshi, is protagonist of this series.

Nadeshiko, a high school student who had moved from Shizuoka to Yamanashi, decides to see the famous, 1000 yen-bill-featured Mount Fuji. Even though she manages to bike all the way to Motosu, she's forced to turn back because of worsening weather. Unable to set her eyes on her goal, she faints partway to her destination. When she wakes up, it's night, in a place she's never been before, with no way of knowing how to get home. Nadeshiko is saved when she encounters Rin, a girl who is out camping by herself. This outdoorsy girls story begins with this first encounter between Nadeshiko and Rin.

Kyotaro Ichikawa, a boy barely clinging to the bottom rung of his school's social ladder, secretly believes he’s the tortured lead in some psychological thriller. He spends his days dreaming up ways to disrupt his classmates' peaceful lives and pining after Anna Yamada, the class idol. But Kyotaro's not nearly the troubled teen he pretends to be…and it turns out Anna's a bit odd herself!

This feisty young wizard will stop at nothing to master the spell that saved her life: Explosion! Megumin, the “Greatest Genius of the Crimson Magic Clan,” has chosen to devote her studies to the powerful offensive magic used by her mysterious savior. Then one day, her little sister finds a black kitten in the woods. But this cat isn’t just a new furry friend—she’s the key to awakening a Dark God!

A terminally ill girl named Himari Takakura is miraculously saved from death by a strange spirit who resides in a penguin-shaped hat. However, in exchange for extending her life, the spirit tasks Himari's brothers, Kanba and Shōma, to seek out an elusive item known as the Penguin Drum with assistance from a trio of strange penguins.

After being in a coma for 17 years, Takafumi's middle-aged uncle suddenly wakes up speaking an unrecognizable language and wielding magical powers.

The Sakuragoaka Girls' Academy curriculum traditionally focuses on the three "R"s of reading, writing and arithmetic, but Ritsu Tainaka wants to add two more "R"s: Rock and Roll! To do that, however, Ritsu has to save the Light Music Club from being shut down due to little problems like not having any other members or a faculty advisor. After strong-arming her best friend Mio into joining and convincing Tsumugi Kotobuki to make it a trio, Ritsu's would-be rockers are soon only one talented guitarist short of the quartet they need for school approval. What they get, unfortunately, is Yui Hirasawa, who's never held a guitar in her life, but she's determined to learn! Will the school halls come alive with the sound of music?

On her first day attending the all-girls Nanamori Middle School in Takaoka, Toyama Akaza Akari oversleeps, to be awakened by her one-year-senior childhood friends: the level-headed Funami Yui and the often self-centered Toshinou Kyouko. Planning on exciting club activities at school, Akari joins the club her older friends have set up. But as it turns out Kyouko and Yui simply took over the former room of the now defunct tea ceremony club for their own Amusement Club. In regard to what the club does, Kyouko explains: "We just hang out and do whatever we want!" This is not exactly what the helpful and energetic Akari had hoped for. Surprisingly a few days later Yoshikawa Chinatsu joins the club even though she mistook it for the former tea ceremony club.

And so the four fun-loving girls could enjoy spending their spare time at the club were it not for the student council, in person of vice president Sugiura Ayano, who does her very best to shut down this unauthorized club.