Lyric discussion by starwanderer 

Cover art for Binary lyrics by Crüxshadows, The

Okay, I understand this perfectly.

The "messenger" refers to Jesus. Christians consider Him both fully human and fully devine, ergo the "binary soul" of "I." Also, humans have both evil and good in their souls, thus, the binary nature of human's souls.

The lyrics present the idea that even Jesus did not fully understand what God's message and purpose was while he was fully human (i.e. while he was on Earth with us) because he is limited just as we are by our nature. Also, the lyrics state that "The wounds I bear/have left me humbled/once a child of divinity." Obviously this refers to his crucifixion.