The medieval land of Parthoris is swept by a mysterious plague. Its infected inhabitants descend into madness. Corvus, the protagonist of the first Heretic, finds a way to escape from his home town, but is still contaminated by the plague. Since he possesses one of the ancient Tomes of Power, he is not immediately affected by the plague; but sooner or later, he will have to succumb to it. Before that happens, Corvus must find who or what was causing the plague in the first place...

Heretic II is a third-person fantasy shooter game with the camera chasing behind the character. The perspective is pretty much the only thing that breaks with the tradition of the series. The core gameplay still consists mainly of exploring the large fantasy-themed levels, using medieval weapons (mainly long-ranged) and spells to deal with the plethora of enemies. Despite the third-person view, jumping and environmental puzzles are used as moderately as it is usual in first-person shooters.