Lyric discussion by exnihilo 

This song is about both Christianity AND the Matrix. The Matrix itself is a distilled version of Existential Philosophy, which is highly compatible with Christianity and was used by Soren Kierkegaard to capture Christianity's main beliefs. Also, Plato's metaphor, The Cave, sounds hauntingly like The Matrix.

This relates to the experience both Neo and any Christian go through when they are presented with the Christian reality. They come to face that everything they've ever held to be true is just a loosely-held illusion.

I've actually heard conversion described quite often like being roused from sleeping in a dream-world. You never look at anything the same way again, which captures Neo's point of view perfectly.

As for the song being about Daniel, that's highly likely. There are a number of allusions in The Matrix to the book of Daniel, one of them being the name of Morpheus' ship, the Nebuchadnezzar. He was one of the kings that Daniel interpreted dreams for.

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