Lyric discussion by Dead Smiley 

Cover art for God lyrics by Smashing Pumpkins, The

I think its sort of about the corruption of the Church. "I hope God forgives me For my transgressions" is maybe about buying forgiveness, a practice from the Church of the middle ages. "When the darkness comes to me And fixes it's gaze on me" is maybe in reference to the Dominicans and the Inquisition? Or perhaps its just a really angst-y song. That interpretation works as well. Pissed off by the pressure of the Church and Sin and Heaven and Hell.