Princess Maker 3 takes place in an alternate world from Princess Maker 1 and 2, as characters from both games (main and side) make appearances throughout the game.
The game begins with the Queen of the Faerie realm speaking to the father figure in this game, addressing the father figure by the profession he chooses. She explains that a certain faerie wishes to become a human princess, and has pleaded with her to come to the human world. She then bestows the girl on the hero, making it his job to raise her to adulthood. To help with the task, a faerie housekeeper by the name of Uzu is assigned to the hero, and thus the journey begins.