Lyric discussion by sawall 

This song is indeed about a spiritual crisis, and what brideonfire writes about is accurate about the basic attitude of the singer and what they're reflecting about. It's also explicitly Christian.

"One more Son" refers to Jesus, the Son of God.

"when there's nowhere else to run / is there room for one more son?" is asking if someone who feels like they're out of options has room for Jesus in their heart.

"shine on in the hearts of men" is a Biblical reference ("For God, who commanded the light to shine out of darkness, hath shined in our hearts, to give the light of the knowledge of the glory of God in the face of Jesus Christ." - 2 Cor.4). There's also a phrase that is translated similarly in more modern translations of the Bible in Matthew 5:16 where Jesus is preaching for his followers to shine in the hearts of others.

Going down this path, "back of my broken hand" can easily be taken to be Jesus' hand, broken by the nail of the Crucifixion.

"don't put me on the backburner" is suggesting one will get lost if you're ignoring Jesus, and if you do, "you're gonna bring yourself down" i.e. become lost.

"over and out, last call for sin" refers to Armageddon. During the Second Coming, the only people who are left are unrepentant sinners (lost), then the battle is won - "while everyone's lost, the battle is won". Even despite the sins ("all these things that I've done") you still win if you've kept the faith ("if you can hold on").

I agree with brideonfire's readings of the "cold-hearted boy" and "I got soul but I'm not a soldier" lines - that the singer isn't a soldier of the Church but still has belief in something that he's trying to sort out.

"time, truth, and hearts" is a reference to Psalm 69, verse 13. Psalm 69 is plea for help to God from a repentant sinner. The story arc of Psalm 69 is very similar to the arc of "All These Things That I've Done." One of the claims at the end is that the sinner will praise God in song.

nice connections! but i don't get how "time, truth, and hearts" relates to that verse...?

This song isn't about god. Everyone thinks that if a song can somehow connect to the bible, than it MUST be about the bible. The songs pretty cutthroat. The songs about being in a relationship with someone that expects too much out of you but you don't know what those expectations are because they won't tell you. "I need direction to perfection.." he's saying he needs that person to tell him what they want him to do to meet those expectations. " don't you put me on the backburner" here he's saying don't just put our problems aside and think...

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