Venturing into the wilderness, the skeptical Ryouta Murakami and the ambitious Kuroneko were on a quest to prove the existence of extraterrestrial life when a tragic accident occurred, reaping Kuroneko of her life and leaving Ryouta in a critically injured state. Ten years have passed since the disaster, and Ryouta is now living a normal life in high school. He vows to prove that aliens are real in honor of his late friend. A transfer student named Neko Kuroha unexpectedly arrives one day, bearing a striking resemblance to the late Kuroneko—even sharing a similar name. Most mysteriously, she seems to possess supernatural powers. As Ryouta takes more interest in Neko, he is drawn into a deadly world where dangerous scientists hunt magic-wielding witches that have escaped from their secret research laboratory. Neko is one of these escapees, but there are many others who are in similar situations, and it's up to Ryouta to protect them from their would-be captors. When he was a child, Murakami was infatuated with a girl he called Kuroneko. She insisted on knowing about aliens and having met them, but no one believed her, even young Murakami was skeptical. One day, she decides to show him the aliens, but an accident occurs and Kuroneko dies while Murakami is left seriously wounded in the hospital. Years go by and Murakami obsesses on finding proof of the existence of aliens because of a promise he had made with Kuroneko. Then, one day, a new transfer student comes to his class, who not only looks a lot like Kuroneko, but is named Kurohaneko! And even though she insists on never having met Murakami before, the girl has superhuman strength and seems to even be able to predict the future! How will Murakami's life change now that he has been saved by this mysterious girl that claims to be a magician?