"The Church acts as a bridge and buffer between the Legion and Arcanum, using a mixture of magic and military training to maintain the balance of power while secretly furthering its own interests."

- Hexen manual

The Church is one of the three institutions that control human society on the world of Cronos, along with the Legion and the Arcanum. Maintaining a fine balance between military and magical discipline, the Church serves as a bridge between the militaristic Legion and intellectual Arcanum, while at the same time pursuing its own secretive goals. They also manage all matters of faith within society, though it is never made clear what the religion of Cronos is.

The institution is led by a Grand Patriarch. At the time of Hexen: Beyond Heretic, the acting Grand Patriarch was the once pious Traductus, who has thrown away his faith and made a pact with the Serpent Rider Korax, pledging his loyalty in exchange for the gift of Unlife. He is likely responsible for the creation of the Dark Bishops.

The Church is a balanced faction, combining elements of the Legion's and the Arcanum's nature. They also wield numerous unique artifacts of mystical power and are able to unlock special properties within certain magic items (such as the Flechette's poison gas cloud). They also possess ancient relics of horrendous power, such as the Wraithverge.