Negi Springfield is a 10-year-old child prodigy graduating from the Magic Academy. He is sent off to become a teacher at a school in Japan known as Mahora Academy to continue his mage training. One year later, two representatives from the Magic Academy come to Mahora and tell Negi that a powerful artefact known as the Star Crystal has disappeared. For unknown reasons, the power of the artefact affects Negi and his students. So he and the class fight off the dark power, while searching for Negi's missing father.