I think this song is about how although all men are created equal and although in our lifetimes we share and experience beautiful things amongst each other, at the end of the day it is buried in our instincts and souls to become greater or lesser than other men through the actions we take and that we, even in small, unconsciously noticed ways we are destined to slowly destroy each other.

I think metalhedscot and newellhp are the most on point. The first thing I thought when I heard this song is religion because he says you should pray for forgiveness and the flood and to end the nightmare (the nightmare is not knowing who to turn to for answers). Also a key verse in the song is "some kind of purpose, a glimpse of light in his void of darkness". What he's saying is that there are many out there who feel alone because they want the true meaning to life, not a bunch promises and rules written by men who may well have been a bunch of crazy-a* schitzophrenics thousands of years ago. He wants us all to pray not to go to heaven but to pray to find others alike us searching for answers in the depths of despair, to find unity among the lost.