Hexen II, like Hexen, utilizes character classes and a hub system. You can play either as an Assasin, a Paladin, a Crusader or a Necromancer (with the Portal of Praevus Mission Pack, you can add a 5th character class, the Demoness). Each class has different weapons and different abilities, magical or physical. The Hub design is extensive and there is a great deal of backtracking involved in the gameplay.

Unlike previous fantasy games from Raven,Hexen II follows closely the real world by modeling Earth's early cultures (Ancient Egypt, Greece and Rome; Mezo-America and Europe of the Medieval Ages). Your goal is to defeat the last of the Serpent Riders, Eidolon (who looks a lot like the Devil of Christianity). On the way to meet him, you must first defeat the Four Horsemen of the Apocalypse (taken from the Bible as well): Famine, Death, Pestilence and War.