Set eight years after Atelier Sophie and four years after Atelier Firis, the story follows the alchemist twins - the reserved but caring Lydie Marlen, and the eccentric, carefree Suelle Marlen who work alongside their father at the family atelier. But due to his inexperience in alchemy they rarely see any customers. While working to hone their skills, the duo uncovers a mysterious-looking painting, and as they reach out to investigate, the girls are drawn inside a world bountiful with rare materials perfect for alchemy.