After Yuko has defeated the evil Rogles, peace descended upon Earth and the magical world of Vecanti. But a new threat has arisen: an enigmatic man named Glames from the Dark World, possessor of a sword named Leethus, is planning to conquer both Earth and Vecanti, convinced that there is no other way to save his world from imminent destruction. A young girl from the Dark World named Cham escapes from Glames, and asks Yuko to help her stop him with the aid of her Valis sword.

Like its predecessors in the series, Valis III is a side-scrolling platform action game. Unlike the previous installments, the player can control three characters in the game: Yuko, Cham (who uses a whip and fights similarly to Castlevania protagonists), and princess Valna from Vecanti, who is weaker physically, but can cast more powerful magic. Each of the characters can equip different weapons and has access to her own magic spells.