Tooru Honda has always been fascinated by the story of the Chinese zodiac that her beloved mother told her as a child. However, a sudden family tragedy changes her life, and subsequent circumstances leave her all alone. Tooru is now forced to live in a tent, but little does she know that her temporary home resides on the private property of the esteemed Souma family. Stumbling upon their home one day, she encounters Shigure, an older Souma cousin, and Yuki, the prince of her school. Tooru explains that she lives nearby, but the Soumas eventually discover her well-kept secret of being homeless when they see her walking back to her tent one night. Things start to look up for Tooru as they kindly offer to take her in after hearing about her situation. But soon after, she is caught up in a fight between Yuki and his hot-tempered cousin, Kyou. While trying to stop them, she learns that the Souma family has a well-kept secret of their own: whenever they are hugged by a member of the opposite sex, they transform into the animals of the Chinese zodiac. With this new revelation, Tooru will find that living with the Soumas is an unexpected adventure filled with laughter and romance.

Ryou Sakaguchi is a totally normal high school student, aside from his single unusual hobby. Sakaguchi is a fudanshi—a man who loves reading boys' love manga, and fantasizing about the gay potential he sees everywhere. He has only one wish before he dies: to find himself some friends that understand his secret passion. His wish comes true, as Sakaguchi begins to uncover a host of interested parties. There's Rumi Nishihara, a closeted fujoshi who is more than eager to discuss the joys of boys' love with Sakaguchi; the flamboyantly gay leader of the school's cooking club, Yuujirou Shiratori, who makes no effort whatsoever to conceal his sexuality; Akira Ueda, Shiratori's diligent admirer, who will do anything for the love of his life; and even the mischievous Daigo, a fellow fudanshi and popular author of boys' love doujinshi. Standing by their sides throughout all the otaku chaos is Sakaguchi's best friend, Toshiaki Nakamura, who only wishes his classmates would start acting more like normal people.

Decades into the future, humanity is under siege by an alien race known as the Novas. These inhuman beings leave devastation in their wake whenever they appear, with the efforts to stave them off becoming known as Nova Clashes. Young women known as Pandoras and young men known as Limiters are implanted with stigmata to give them superhuman powers and are trained in military academies, where they must learn to work together if humanity is to have a chance of surviving. Freezing tells the story of Kazuya Aoi as he sets out for his first day at the West Genetics military academy, right when a battle royale is being undertaken by the Pandoras. It is here that he mistakes Satellizer el Bridget—a powerful Pandora known as the Untouchable Queen—as his deceased sister and embraces her. Though he costs her the match, she finds that his touch doesn't drive her away and decides to take him as her Limiter. The only question is whether or not their partnership can survive the machinations of their upperclassmen and the impending battle with the Novas…