The game's story takes place about four years after the beginning of Atelier Ayesha: The Alchemist of Dusk in a far away place to the west of the Twilight Land where the local administration hires two new alchemists, Escha and Logy as members of their R&D division. While learning the ropes of their new occupation, Escha and Logy gather friends and companions as they unlock the secrets of the nearby ruins and help the citizens in a world that is still recovering from a catastrophic event known as "The Dusk".