Magickal alignment is an important concept in Eternal Darkness, and it affects many aspects of the game including combat, puzzle solving, and the story. Alignment is based on the rock-paper-scissors like relationship between the three main Ancients. Ulyaoth defeats Chattur'gha, Chattur'gha defeats Xel'lotath, and Xel'lotath defeats Ulyaoth. Pious Augustus, under the player's direction, chooses one of the three Ancients and this determines the alignment of enemies and puzzles the player encounters throughout the rest of the game. The player gains an edge by using spells and enchanted weaponry aligned to the Ancient that defeats Pious'.

Additionally, spells aligned to Mantorok are strong against the other three Ancients and may carry additional benefits.