Charlotte follows the story of four students in an alternate reality from Hoshinoumi Academy, a school founded to protect children with special abilities that develop during puberty, as they search for and protect others like them throughout Japan.
These students include Yū Otosaka, a boy with the power to control another person, albeit only for 5 seconds and only when directly looking at the target, Nao Tomori, who uses her power to become invisible to one person she chooses in order to convince others to listen to her, Jōjirō Takajō, with the power to move extremely quickly making it look like teleportation, and Yusa Nishimori who is usually possessed by her deceased pyrokinetic sister, Misa, due to her ability as a medium.
