A tragic accident that took the life of his childhood friend, Kuroneko, fuels Ryouta Murakami to dedicate his life to what she believed in—aliens. Ten years later, Ryouta is the sole member of the Astronomy Club, and spends late nights hoping to find proof of extraterrestrial life. One day, a girl named Neko Kuroha, who looks suspiciously like Ryouta's late friend, transfers into his class. Denying any memory of knowing Ryouta, she disappears after giving him an eerie warning. It is later revealed that Neko is a witch—a scientifically enhanced magic wielder—who escaped from being experimented upon in a secret research laboratory.

Soon, other witches find their way to the Astronomy Club in an attempt to escape the tragic fate that awaits them. Witnessing the cruelty the young girls were subjected to, Ryouta takes it upon himself to protect the witches against their oppressors, and uncover the mystery behind Neko's bizarre resemblance to Kuroneko.