Charlotte follows Yuu Otosaka, a gifted student who can briefly take over another person's mind and body for five seconds at a time. He uses that power to cheat through exams and glide through high school, until Nao Tomori, the sharp-witted student council president at Hoshinoumi Academy, exposes his trick and forces him to transfer. Once there, Yuu learns that Hoshinoumi is a hidden refuge for teenagers with supernatural abilities, and that the student council exists to track down ability users who abuse their powers and protect those who need help. Working alongside Nao and the rest of the council, Yuu begins helping the group search for new ability users and intervene before their powers cause harm. What starts as a cynical arrangement slowly pulls him into the lives of people burdened by extraordinary abilities, and the deeper the council digs, the more tangled and complicated the truth behind those powers becomes.
