The story of Atelier Rorona takes place in the poor, isolated kingdom of Arland. A travelling alchemist visits the kingdom and shows its residents how to use the abandoned technological relics of nearby ruins. This begins a new era of prosperity within the kingdom. As a reward, the king allows the alchemist to open an alchemy workshop within the kingdom. A great many years later, the workshop is all but forgotten. One day, the workshop receives an ultimatum from the king: prove its usefulness in three years time or face closure. The current owner abandons the workshop to Rororina Frixell, her young and inexperienced apprentice. Known to her friends as Rorona, the game follows the alchemist-in-training and her companions as she tries to complete twelve challenges in order to keep her workshop open.