Junketsu no Maria tells the story of Maria, a young and powerful witch residing in medieval France during the Hundred Years' War.
Disgusted by the brutality and suffering caused by the ongoing conflict between France and England, Maria uses her magic to actively prevent battles and maintain peace.
Her interference draws the ire of Heaven, leading the archangel Michael to forbid her from using her powers, threatening to strip her of her magic if she loses her virginity.
Despite being branded a heretic, Maria persists in her attempts to stop the war, even as the Church plots to end her interference once and for all.
The anime explores Maria's struggle to protect the innocent and uphold her ideals in a world consumed by war and religious dogma, facing opposition from both earthly and heavenly powers.