In Nestor Stephen associates darkness with mysterious metaphysical truth. His symbolism inverts a standard biblical identification of truth with divine light.
The opening verses of John's gospel proclaim: "In the beginning was the Word, and the Word was with God, and the Word was God. . . . All things were made by him; and without him was not any thing made that was made. . . . And the light shineth in darkess; and the darkness comprehended it not" (1:1-5). Unlike this Christian Logos, Stephen thinks of a soul of the world that is "obscure," "a darkness shining in brightness which brightness could not comprehend."
He also thinks of the Pharisees not comprehending the "long look from dark eyes" that they received from Jesus. He rejects Mr. Deasy's condemnation of the Jews: "— They sinned against the light, Mr Deasy said gravely. And you can see the darkness in their eyes." He thinks of Averroes and Moses Maimonides (one of them Muslim, one Jewish) as "dark men in mien and movement." He thinks of his own "mind's darkness" as a Blakean "underworld, reluctant, shy of brightness, shifting her dragon scaly folds." And he thinks of the secrets that sit in the "dark palaces" of his and Sargent's hearts.
Clearly, this inversion of traditional religious symbolism has much to do with Stephen's use of traditional religious language to articulate an idiosyncratic poetic vision. It also becomes one basis among many for the metaphysical union of Father and Son that the novel is planning for Bloom and Stephen. Both men are dressed in dark clothes througout the day, and the darkness of Jewish eyes that Mr. Deasy finds so suspicious becomes one source of Bloom's mysterious attraction. In Ithaca, Stephen considers Bloom's "winedark hair."
 Thornton notes some critical efforts to connect Stephen's transvaluation of darkness with certain Neoplatonic Christian writers (the pseudo-Dionysius, Henry Vaughan) who propounded a via negativa of transcending sense perception and reasoning to enter "the darkness of unknowing."