On a rainy morning in Tokyo, Takao Akizuki, an aspiring shoemaker, decides to skip class to sketch designs in a beautiful garden. This is where he meets Yukari Yukino, a beautiful yet mysterious woman, for the very first time. Offering to make her new shoes, Takao continues to meet with Yukari throughout the rainy season, and without even realizing it, the two are able to alleviate the worries hidden in their hearts just by being with each other. However, their personal struggles have not disappeared completely, and as the end of the rainy season approaches, their relationship will be put to the test.

Haruka Shinozaki has been interested in the class representative, Akiho Kousaka, since his first year in high school. She is attractive, good at sports, and is an all-around model student. Since they are in the same class this year, Shinozaki decides to confess his feelings—and, to his shock, Kousaka agrees to be his girlfriend! However, he finds that Kousaka is a bit stranger than he first thought: this seemingly perfect girl has never been in a relationship. But even though she is inexperienced, she vows to please Shinozaki in every way she can... such as learning multiple sex positions or his fetishes. Shinozaki tries to assure her that her studies into such subjects aren't necessary, but Kousaka devotes herself to making him happy in more ways than one. [Written by MAL Rewrite]

After the defeat of Myouri Unzen at the hands of Medaka Kurokami and her Student Council, peace has returned to Hakoniwa Academy—at least, for a short while. Soon, Medaka, Zenkichi Hitoyoshi, Kouki Akune, and Mogana Kikaijima find themselves wrapped up in another sinister scheme, known as the "Flask Plan," led by the school's principal himself. However, the council's first problem is to deal with a whole new group of superhuman students calling themselves the "Thirteen Party," led by the egotistical but powerful Oudo Miyakonojou. With the mysterious Flask Plan, Oudo's tyranny, and the resurfacing of an old enemy, the state of Hakoniwa Academy is far from tranquil, and Medaka and her companions have their hands full as things only get a lot more abnormal. [Written by MAL Rewrite]

Medaka Kurokami is, in the truest sense of the word, perfect. Beautiful, intelligent, and athletic, Medaka's dream is to make others happy. So when she runs for Student Council President of the prestigious Hakoniwa Academy, winning the election with 98% of the votes is only to be expected. The very first thing the boisterous new president does is set up the "Medaka Box," a suggestion box allowing students to submit any kind of request for assistance. Together with the cynical Zenkichi Hitoyoshi, her childhood friend who has been strong-armed into helping, Medaka fulfills these requests at a ridiculous rate. For every job completed, she adds flowers to the student council room, with the aim of filling the entire school. However, the two are about to find out that helping others may be a lot harder than they think as they begin to uncover a devastating plan centering on the academy and even Medaka herself! [Written by MAL Rewrite]