Lyric discussion by GodofGuitar 

As usual, the song is partly christian, but not really. Petrucci throws Christian meanings in there, but always compromises the overall meaning. Anyways, this was quoted from Wikipedia about this song:

"The lyrics tell a story about a man who, at the moment of death, sells half of his soul to a "dark master" in order to gain power to stand in the way of the servants of an evil fallen angel, who are paving the way for their master's coming. The man is seeking revenge on the one who killed his beloved, and also seeks redemption for humanity. At the end he retains his own soul and does not fight for his master.

It is notable that the story told in the song is strikingly similar to the story of Ivan Isaacs told in the Korean comic Priest. Tokyopop, the publisher of Priest, provides a short résumé of the story that even shares certain expressions and phrases with the lyrics of In the Presence of Enemies. John Petrucci also said in an interview that one of the songs in Systematic Chaos was based on a manga [Priest]." Go here to see the Priest references: faq.dtnorway.com/question/1098

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