The game takes place after Atelier Elie: The Alchemist of Salburg 2. After meeting Marlone in the academy of Kentonis, Elfir "Elie" Traum gets robbed on her way back to Salburg. The academy proposes that if she can create a "Origin Flame(原初の炎)" within 3 years, they will help her with money and et cetera. The two alchemists Marlone and Elfir then teams up to create an Origin Flame and opens their own workshop.