Wild Arms 3 (titled Wild Arms Advanced 3rd in Japan) boasts major technological improvements and a number of new gameplay elements. Featuring "stroke-shaded" animation-style graphics, a "Wild West" setting, and a completely 3D game engine (not just for battles, as in the previous games).

The game takes place on a version of the planet Filgaia from the Wild Arms series, a place that is desolate to the point of even its seas consisting of sand, supposedly the result of an ancient war. Four Drifters find themselves chosen to wield the power of the planet's spiritual protectors, the Guardians, to stop a prophesied but unknown menace to their world. As they adventure together, they are opposed by other Drifter teams, a trio of fanatical scientists called the Prophets, and the Demons of Filgaian legend. The four adventurers eventually make startling discoveries about their world's true history, and their personal connections to it.