The story takes place 5 years after the previous game, Atelier Rorona. It begins with Totori in the fishing village of Alanya, her hometown, and will come to a close after five years pass. Totooria Helmold, Totori for short, is Rorona's student who is looking for her missing mother. After the events of Atelier Rorona, Rorona has been traveling across Arland teaching alchemy. One day, Totori's dad is fishing outside on a dock when his hook catches something big. When they reeled the line in, they found a hungry Rorona. That is when Totori learned about alchemy and became her student. Ever since then, Totori has been learning alchemy on her own.

Totori's older sister, Cecilia believes that their mom is dead. However, Totori still thinks she is alive, so she eventually travels to Arland and meets Cordelia and reunites with Rorona. Cordelia works at the castle front desk next to Filly, Esty's younger sister who is now taking over her job since she has mysteriously disappeared. She hands out certain tasks which can be completed to upgrade your Adventurers License. By upgrading your license, you can travel to farther lands. By following her mother's footsteps as an adventurer and improving her alchemy skills, you follow Totori on her journey to find her beloved mother.