The game's story takes place about 4 years after the beginning of Atelier Ayesha: The Alchemist of Dusk in a far away place to the west of the Twilight Land. Because of "The End of Dusk", the people of the land have rediscovered the lost art of alchemy.
Atelier Escha & Logy will allow players to choose between two protagonists. The main storyline will remain the same regardless of who is chosen, but certain events and ending will only be available on a particular protagonist.
Source: Wikipedia, "Atelier Escha & Logy: Alchemists of the Dusk Sky," available under the CC-BY-SA License.