The story is set on the floating island of Yen, which houses a magical school, approximately three hundred years before the events of Lunar: The Silver Star. It follows Elie and Rena, two girls from the farming town of Burg who are recruited to attend the school, along with their classmate Senia, a beastwoman. They are assigned to the most troublesome class, whose students are rowdy and undisciplined. As the trio navigates school life, they face challenges from both their eccentric instructors and a group of bullies, Ant, Kule, and Rick. Later, a quiet but naturally gifted mage named Wing joins the class.

The narrative centers on the students learning to work together and understand one another. Their adventures escalate when the Vile Tribe, led by the power-hungry Memphis and his second-in-command Barua, threatens the island and the school. The students must set aside their differences and use their developing magical abilities to protect their home. Key story arcs include the group's initial struggles to find order in the chaotic school, the deepening friendships among the main cast, and the eventual confrontation with the Vile Tribe, which forces them to grow from squabbling classmates into a cohesive team capable of defending Yen.