Lyric discussion by neoritter 

I really don't think people are taking this song in the correct sense. I don't think this song is about Christianity as a whole or religion as a whole. It's about some of those fanatical denominations and sects of Christianity or religions that pop up. And I am not going to point fingers at any in particular because that would bog me down in unrelated topic. First think about the title. Heresy, which means, 1. Adherence to a religious opinion contrary to church dogma. 2. an opinion or doctrine contrary to church doctrine. 3. dissent from a dominant theory, opinion, or practice. This automatically tells you he's speaking of some sort of heretical belief within some sort of religion. First, we need to learn to differentiate between "God" and "god." Let's start with the latter; "god" refers to a deity that people might worship and is not a proper noun and refers to a thing, a word versus a name. Now the former, "God" is a proper noun or a name to simplify and is refering to the Christian god (notice the lack of capitalization there) God. So where you find Trent saying, "your" or "a" before "god" he is using the word not the name. And in other cases he is using the god's name God. So lets replace "god" with "deity" and "God" with "Yahweh". Example: "He dreamed a god up," change to "He dreamed a deity up," and "God is dead" to "Yahweh is dead." This will make the song make a little more sense and help you to understand my explanation of the song. Now on to actually explaining the song. And as such please note which version I am using by noting the capitalization.

/He sewed his eyes shut, because he is afraid to see,/

Trent speaks of the fear people have of the truth, particulary in a later song he created called "Right Where it Belongs." These two lines mean that this person whoever "he" is has decided to blind himself to the truth.

/He tries to tell me, what I put inside of me, He's got the answers, to ease my curiosity, He dreamed a god up, and called it Christianity./

This person after refusing to see the truth has created his own answers and truths, and has decided to tell others what he thinks. Some sects do not pass judgement on some questions because they are not of any significance and are up to the judgement of the individual to decide. This person has answers to some of these unanswered questions and others. Either because he believes what he is preaching is Christian or because he feels it would draw more followers has decided to call his "religion" Christianity.

/God is dead, and no one cares, if there is a hell, I'll see you there./

Trent or the person in this story referenced in the first few lines has discoverd that what he got into is not Christianity and that the real god, God, is dead to the new leader's followers and those followers don't or seem to not care. The last two lines here I think affirms some sort of belief in god or Christianity. The last two lines Trent is saying that due to this group's heresy they are going to hell and because he as either taken part in it he will be there with them.

/He flexed his muscles, to keep his flock of sheep in line, he made a virus, that would kill off all the swine, His perfect kingdom, of killing, suffering and pain, demands devotion, atrocities done in his name./

Obviously, his following has grown enough to include people who are not as fanatical or devoted to the religion, and as such some sort of dissent from within has formed. To keep any rebellion from happening he must remove the dissenters or the "nonbelievers" and scare the people who might go either way from becoming nonbelievers themselves. The "virus" is a representation of whatever he may have used to remove these nonbelievers. This kingdom of killing, pain, and suffering is of the nonbelievers and the devotion he demands is by the true followers of his order.

/God is dead, and no one cares, If there is a hell, I'll see you there, Your god is dead, and no one cares, if there is a hell, I'll see you there./

/God is dead, and no one cares, If there is a hell, I'll see you there, (your god is dead) God is dead, (and no one cares) and no one cares, (drowning in his own hypocrisy) if there is a hell (see you) I'll see you there, (you there)/

The last section of this song is basically the same as the chorus except now the hypocrisy of this man's god is evident and his followers still have not realized it.

Now this is my own interpretation, but I think the basics of the song is not that religion or Christianity as a whole is bad, but that there are religions or denominations of Christianity that are wrong and hypocritical. I've never fewed as Trent as anti-religous but rather anti-corruption, so against corrupt religions. I think he may have realized that people have put religion on some pedestal and whether religion is a product of God/gods or man, religion is not whats evil and wrong but the people that use it for such ends. I've used the cliche sentence, the sword isn't inherrently evil, but the person that wields it.

@neoritter Wonder if Trent would agree? What you said makes a lot of sense. I know personally how mainstream Christian doctrine was used and manipulated by the person I trusted most in this world, to single handedly rob me of my entire life, including my own children. Even more shocking, was that many close to me who boast about their Christianity, abandoned what they preached when he threatened them if they helped me. I am left asking why? That is when I realized my story has been told through Trent Reznor. Sometimes his music...

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