Kyoshiro to Towa no Sora revolves around the life of Kuu Shiratori, a seemingly normal high school girl who enjoys her school life in the giant city Academia, which is thought of as a symbol of recovery for humanity since already ten years have passed since the greatest disaster mankind had ever seen, occurred. Kuu has recently been having a recurring dream where a prince meets her and takes her away. One day, while all the students at her school are preparing for the upcoming school festival, the prince, whom she has met several times in her dreams, appears. The prince, Kyoshiro Ayanokoji, requests of her just as he had done in Kuu's dreams, "Let's go... together..."

Kurotori Chiyoko, a 5th-grader in elementary school, loves the occult. One day, a friend requests her to do a love fortune-telling. Chiyoko tries to summon Cupid, but thanks to a stuffy nose, accidentally summons a witch named Gyubid instead! From that day on, Chiyoko starts learning witchcraft from Gyubid, the self-proclaimed hottest instructor of the magic world. The training regimen is tough, and punishment for slacking is harsh. Fortunately, Chiyoko is able to keep her extra-curricular studies secret, aided by the fact that no one else can see Gyubid.

Hidden away on a remote mountaintop, the Kokoro Library struggles to attract many visitors. Nevertheless, it is the home of sisters Iina, Aruto, and Kokoro, who consider it their mission to keep the library running in their parents' stead. Kokoro has long dreamed of becoming a librarian at the library with the same name as her, and tries her best to keep up with her older sisters. Due to the lack of patrons, the girls mainly spend their time sipping tea, chatting, and reading. However, as the number of mysterious visitors progressively increases, Kokoro begins to learn about the strange history of Kokoro Library—a place where small miracles seem to blossom.

Kouta has girl troubles of the supernatural sort. For some reason, he keeps attracting the attention (and affections) of animal spirits! Having spent most of his life in the country, Kouta is understandably nervous when he moves in with his grandma to attend a high school in the big city. He hoped to make a good impression, but having Chizuru, a beautiful fox spirit, hanging off his arm didn't seem to be the sort of image he wanted to have. She's not alone in her love for Kouta, either. Nozomu, a wolf spirit, as well as other youkai have their sights set on the hapless country boy.