"Charlotte" is a 13-episode anime series set in a world where certain adolescents develop supernatural abilities upon reaching puberty. These powers, however, are temporary and fade as they grow older. The story centers on Yuu Otosaka, a high school student who possesses the ability to temporarily take control of another person's body for five seconds. Initially, Yuu uses this power to cheat his way into a prestigious school, but his life takes a dramatic turn when he is confronted by Nao Tomori, a girl with the ability to become invisible to a single target. Nao is a member of the student council at Hoshinoumi Academy, a school established to protect and guide students with special abilities.

Yuu is forced to transfer to Hoshinoumi Academy and join the student council, which also includes Joujirou Takajou, who can move at superhuman speeds but only in short bursts, and Yusa Nishimori, a girl who channels the spirit of her deceased older sister, Misa, who was a talented singer. The council's primary mission is to locate and protect other ability users, ensuring they do not misuse their powers or fall victim to exploitation by external organizations. As the series progresses, Yuu and his companions uncover darker truths about the origins of these abilities and the experiments conducted on children to artificially induce them.

The narrative takes a significant turn when Yuu discovers that his younger sister, Ayumi, who initially appears to have no powers, is revealed to possess the ability to heal others at the cost of her own health. Tragically, Ayumi is killed in an accident, leading Yuu to spiral into despair. However, it is later revealed that Yuu's true ability is far more potent: he can "plunder" other abilities permanently, making him a target for those seeking to exploit his power. This revelation ties into the broader mystery of Charlotte, a comet that passed by Earth years ago and is believed to be the source of these abilities.

In the final arc, Yuu embarks on a global mission to plunder the abilities of every user before they can be misused, a journey that takes a heavy toll on his mental and physical health. The series concludes with Yuu successfully completing his mission but losing his memories in the process. Nao, who has grown close to him, helps him rebuild his life, offering a bittersweet yet hopeful resolution. The story explores themes of responsibility, sacrifice, and the consequences of power, wrapped in a blend of drama, action, and moments of lightheartedness.