Atelier Iris 3: Grand Phantasm
The story takes place around a city called Zey Meruze, that resembles Venice in that it is crisscrossed by water channels (with Fairies offering a gondolier service.) However, Meruze also has portals to other dimensions, called "Alterworlds" where, for some reason, humans can't stay for more than a short time (they eventually are magically transported out.) Iris (who in this game is still an amateur alchemist) and her friends Edge and Nell work as "raiders" for the Raiders Guild, an organization that performs tasks for people for a price. Usually these involve missions into the Alterworlds, but can also be as mundane as finding missing pets.
The game follows Iris's team as they rise through the Guild's ranks. The real story, however, involves a sealed book that Iris owns-- and which contains an enormous power that can only be released by finding eight "gem-like fragments," so she endeavors to find all eight of them.