Ayakashi are strange, supernatural creatures invisible to the majority of people. Though most are harmless, some ayakashi attack humans to devour their life force. Exorcist ninjas are tasked with protecting people from these spiteful spirits. Matsuri Kazamaki is a young exorcist ninja born to a prestigious clan. His childhood friend, Suzu Kanade, is an ayakashi medium—an individual with immense vitality that attracts ayakashi. Matsuri deems all ayakashi threatening and wishes to keep Suzu as far from them as possible, but this clashes with her desire to remain close to them. One day, the pair encounters Shirogane, the King of Ayakashi, who is hellbent on consuming Suzu. As she is about to be eaten, Matsuri comes to the rescue and manages to seal the ayakashi's powers—but not before Shirogane takes revenge by turning him into a girl! Until he finds a way to transform back, Matsuri must adjust to his new, peculiar lifestyle while fighting against hostile ayakashi. Moreover, Suzu is now conflicted about her feelings toward Matsuri—further plunging their relationship into a state of ambiguity.

Osamu and Youko Sonoyama want more than anything to adopt every child from Soramame House, but the wealthy couple can only pick one due to their increasingly old age. While they contemplate this delicate decision, one child's alluring beauty and gentle soul instantly draw them in. Two months later, the Sonoyamas welcome 13-year-old Hitori into their warm and loving home. However, Hitori's humble and overly polite exterior is merely a masquerade. In reality, Hitori is a carefully crafted character played by identical twins Migi and Dali. For them, being the ideal child of this kind couple is merely a stepping stone to infiltrating a certain quiet town. While dutifully protecting their cover, the twins work toward their true objective: to discover the truth behind a past incident that left them with a burning desire for vengeance.

An arrogant scientist awakens in the middle of a muddy pigpen, and the last thing he remembers is eating a raw pig liver and collapsing in the subway. He quickly gathers that he has turned into a pig and is now in a strange fantasy land. As he struggles to grasp reality, a young girl named Jess comes to his aid. Jess happens to be a Yesma—a discriminated class of servants distinguished by their telepathic abilities and the silver collars around their necks. Despite his inappropriate thoughts about her, Jess makes sacrifices for his sake, and the pig resolves to repay her the best he can within the limits of his new body. But Jess' generosity does not absolve her from the prejudice the Yesmas face daily, and the pig begins to suspect that Jess is in greater danger than she thinks. While he wants to visit the royal capital and beg the king to change him back into a human, the pig realizes that he cannot simply turn his back on his kind savior.

Impressed by Nanao Hibiya's skill with a sword, Kimberly Magic Academy instructor Theodore McFarlane saves the samurai from certain death amid a fierce battle. With his encouragement, Nanao enrolls in the academy, where she instantly becomes a celebrity after she and four of her peers save a student from an enraged troll. Under the leadership of Oliver Horn, a young man who seems to hide a troubled past, Nanao and her newfound friends start their magical apprenticeship at Kimberly—where only four out of five students make it to graduation in one piece. It does not take long for Oliver and his friends to experience the dangers of the academy firsthand, as a near-death encounter in the labyrinth under the school leaves Nanao grappling with her bloody past. The inexperienced yet determined students must stick together if they want to have a chance to survive and uncover the mysteries that the academy holds.