New species include the Shell Clan, a race of giant armadillos, and the Creeping Clan, a monarchy of artisan frogs. The Dragon Clan from Breath of Fire has all but perished, leaving only scattered statues as proof of their existence. A new religious idol named St. Eva has replaced the Dragon God, and the St. Eva church is rapidly becoming popular all over.
Long ago, a demon attacked the woodland town of Gate. According to local legend, a huge dragon suddenly appeared and banished the demon away. The dragon can still be found slumbering on the outskirts of Gate, where it guards the entrance to the demon realm.
Ryu begins the game as a young boy, the son of a priest in the town of Gate. When his sister Yua goes missing, Ryu's father (Ganer) asks him to fetch her before she gets into trouble. Ryu's search eventually leads him to the wilderness outside Gate, where he finds Yua napping beneath the head of the sleeping dragon. Acting on Yua's advice, Ryu follows suit and falls asleep under the dragon. When he awakens, his family has disappeared, and no one in town recognizes him. Later that night, a young orphan named Bow decides to loot the church. Finding nothing of interest, he decides to accompany Ryu on his way to another town.
Flash forward to many years later, Ryu and Bow are living in Hometown, performing odd jobs for the Ranger's Guild. After an item is stolen from the home of wealthy man, Bow is falsely accused of the theft and forced to flee. With the authorities out looking for him, Bow is left with little recourse but to go into hiding, leaving Ryu to find the real thief.