Charlotte takes place in an alternate reality where a short-period comet called Charlotte passes near Earth every 75 years. When this happens, it spreads dust onto the Earth, which causes a small percentage of adolescent 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 others. Although hoping to use his ability to fraudulently live a carefree high school life, he is exposed by Nao Tomori, a girl who can make herself invisible to a specific target. She forces him to transfer to Hoshinoumi Academy (Hoshinoumi Gakuen, "Sea of Stars Academy") and join its student council, of which she is the president.