Charlotte follows Yuu Otosaka, a teenager who uses his ability to possess others for five seconds to gain an advantage in life.
However, his secret is discovered by Nao Tomori, the student council president of Hoshinoumi Academy, a school for adolescents with special powers.
Forced to transfer to Hoshinoumi, Yuu joins the student council and helps Nao find other ability users who are misusing their powers.
As they investigate, they uncover a deeper and more complex situation than they initially anticipated, facing unforeseen challenges and dangers while trying to protect those with abilities.