When a girl in the village falls ill after a birthday party, the Hero has to go in town to get medicine. And then, event after event, gets on a quest that will reveal the history of this village in the forest, of the villagers, of the world around them.

At the beginning of the game, the player must create the Hero, by choosing a male or female of one of the four races in the Crystal Chronicles universe: the swift Selkies who can double jump and are efficient archers, the knowledgeable Yukes and their higher magick potency, the strong Lilties for the melee fights, and the skilled Clavats who can do a bit of everything.

The game itself consists of adventuring through dungeons, fighting various foes and bosses by using melee or ranged attacks and various spells, and completing some puzzles. In doing so, the player can hire up to three customizable bodyguards to accompany the main character. It is possible to take control of any of these characters at any time in the game. More bodyguards can be created and can be switched in and out of the party.

In the main town there is also a Quest Shoppe where only one character can enter and complete various tasks to gain money and rare materials to create new equipment.

A multiplayer mode can be accessed at any Save Point via Wi-Fi or Wireless internet connection, and can invite up to three friends (who take the places of the bodyguards) in the game. The new players can help in the dungeons and in the quests, there are also some versus quests that oppose the players.