Charlotte takes place in an alternate reality where a short-period comet called Charlotte passes near Earth once every 75 years. As this happens, it spreads dust onto the Earth, which causes a small percentage of preadolescent children who inhale the dust to manifest superhuman abilities upon reaching puberty. The story follows the protagonist Yuu Otosaka, a boy who awakens the ability to temporarily possess another person for five seconds. Although hoping to use his ability to fraudulently live a carefree high school life, he is unexpectedly exposed by Nao Tomori, a girl who can make herself invisible to a specific target. She forces him to transfer to Hoshinoumi Academy (星ノ海学園 Hoshinoumi Gakuen, "Sea of Stars Academy") and join its student council, of which she is the president. Also on the student council is Jōjirō Takajō, a boy who can move at uncontrollably high speeds. The student council's main objective is to ensure the safety of ability users from organizations who seek to exploit their powers. In doing so, the student council warns ability users of the potential danger of using their abilities openly. This leads the student council to Yusa Nishimori, a pop singer who has the ability to channel the spirits of the dead as a medium. Yusa's dead older sister Misa frequently makes use of this ability to freely possess her at any time, which allows Misa to use her own ability, pyrokinesis. Nao soon arranges for Yusa to transfer to Hoshinoumi Academy and join the student council.