Adol Christin's long-time friend, Dogi, wishes to return to his home town of Redmont after hearing about strange disturbances that are happening there. Always looking for an adventure, Adol joins him and soon finds out the cause of this new evil.

The gameplay of Ys III diverged significantly from other games in the series; it utilizes a side-scrolling camera angle and platformer elements similar to that of Zelda II: The Adventure of Link.