Junketsu no Maria is set in medieval France during the Hundred Years' War, where Maria, a powerful young witch, lives with her two familiars and watches the conflict ravage the countryside. Horrified by the suffering caused by the fighting between England and the French, she repeatedly uses her magic to stop battles, protect the innocent, and push both sides toward peace. Her actions, however, draw unwanted attention from Heaven. The archangel Michael is dispatched to keep her from meddling in human affairs, and he warns Maria that her powers will be taken away if she loses her virginity. Branded a heretic by those who fear her influence, Maria refuses to back down and continues to defy both divine authority and the brutal logic of war.
As the fighting drags on, the Church begins to plot against her in an effort to remove her magic and end her interference once and for all. Caught between angelic judgment, ecclesiastical persecution, and a war that consumes the powerless, Maria holds onto her belief that even a witch can fight for peace, no matter the cost.