The main character Ray and his party of Aqutallion warriors embark on a quest to find and destroy Homncruse, the evil power threatening their world. Ray begins his journey alone on a tiny island, but eventually he meets his friends and fellow Aqutallion warriors: Tina, Cody, Leona and Dan, and even creates a town for the victims of Homncruse’s evil to live.
Villains encountered along tend to range from comical, such as Cat Boo and Badbad, to the more sinister elite generals of Homncruse. Initially all the teens are considered Pennon, the lowest rank of warrior. Before they can destroy Homncruse each of them must undergo a trial at their respective temples hidden around the world to receive the secondary powers of Banalet. Dan is an exception because he is the descendant of the Prosperous Wise Man clan of Aqutallion.
When Ray, Tina, Cody, and Leona achieve the status of Banalet and are united by the powers of Dan, Aqutallion is reborn and the group gains incredible powers. Secret of the Stars uses a turn-based RPG battle system where actions in battle are selected through a menu and actions are presented at the end of the turn. Gameplay switches between two parties throughout the game and certain areas are inaccessible without the right party.