Maybe I'm over simplifying things, but to me it's about a friendship or relationship where one of the people has suddenly found religion, and bafflingly become someone completely different from who the other knew. The system only dreams in total darkness perhaps being an admission that the person who found god must have been so low that the songs protagonist can't even comprehend. Like, he's saying you don't need god, but at the same time saying, how did I not know how empty you were inside. That's just a cursory analysis.
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