While you were battling the evil forces of D'Sparil, the other Serpent Riders were busy sowing the seeds of destruction in other dimensions. One such dimension is the decaying world where Hexen takes place. A world littered with the mangled corpses of nonbelievers and inhabited by the undead followers that executed them. Only three humans; a warrior, a mage and a cleric; have escaped the leaders' vicious spell. Now these brave souls have sworn to crush the evil regime that threatens to destroy the world forever. Separated upon entering the mystical portal, the three are forced to attempt on their own what they had hoped to do together: find Korax's stronghold, destroy him and restore order in the physical world. Become one of 3 heroes. Wield superhuman powers and lethal weapons. Walk. Run. Fly. Look all around. Inflict serious pain. Pillage your way through earthquakes, crumbling bridges and fog. Track down powerful artifacts and cast wicked spells. Four sick individuals can wreak havoc via network, two by modem.

Following the tale of D'Sparil's defeat in Heretic, Hexen takes place in another realm, Cronos, which is besieged by the second of the three Serpent Riders, Korax. Three heroes set out to destroy Korax. The player assumes the role of one such hero. Throughout the course of his quest, he travels through elemental dungeons, a wilderness region, a mountainside seminary, a large castle, and finally a necropolis, before the final showdown with the Serpent Rider.