Lyric discussion by InsanityIsBliss 

This song has one central theme - It is meant to speak out against war and violence in general.
The references to religion and Jesus are used only to back up the main point. He uses religion to back up his point by showing how much people try to justify war with ideas such as "the end justifies the means" ("War/ The only way to Peace/ I don't fall for that"). "Gracious even God/ Bloodied the cross/ Your sins are washed enough” - This section is written from the point of view of someone defending war by the idea stated above: arguing that violence is necessary (Jesus died to save us). "Your sins are washed enough" - suggests that God forgives those who do evil things with good intentions, and in order to achieve a good goal - ("Then say forgive me, forgive me"). "The chosen one" is not Christ; he is referring to the listener. Dave is accusing us of trying to force are views and customs upon others. "You're righteous, so righteous/ You're always so right" - This sarcasm, he is trying to say that we each think that we are always right. MISC. "Here there is more than is showing up/ Hope that we can break it down/ It's not so black and white" - This is trying to tell people that they need to keep an open mind and be able to adopt the point of view of others and try to understand them rather than reject them. Specifically "It's not so black and white" is suggesting that we often see our own views as absolutely right, while regarding opposing views as absolutely wrong. "Mother's cry/ "Is hate so deep/ Must a baby's bones/ This hungry fire feed?" - This is a reference to war; it describes how the desire of some to fight requires the lives of young men. The "baby" is a young man that is being sent into war by the choice of someone else.

P.S. This is entirely my opinion. (Sorry about the length, I tried to be thorough.)

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