The game follows the girls' search for their guide and companion, Mokona, who has disappeared into the Spirit Forest. They must venture out to find him, exploring a small interconnected world with various buildings that offer rest, shops where items can be bought, and characters who provide hints and advice.
During battles, random effects sent by Mokona may appear instead of selecting a character, such as health restoration or an instant kill. Negative effects like drained health also occur. The girls must choose from standard commands like attack, magic, item, and flee, or take advantage of the unexpected effects to overcome challenges.