Lyric discussion by offtehdeepend 

Cover art for The Plague lyrics by As I Lay Dying

I may be completely wrong, but I think the song is about corruption in religion. Tim's saying that we've lost sight of what God really wants in favor of the agendas of religious leaders ("Another blind guide replacing divine eyes.") He encourages Christians to look beyond what is taught to them every Sunday and instead think for themselves and think about what God actually wants, not what our religious leaders or what we personally want and try to pass off as God's will. ("I still believe that there is hope for us, but I believe we must look outside the sanctuaries of oppression that have brought our world so much pain....")

Granted, there are a few lines that I can't figure out in the song, such as "Reach out your hand, only to be plagued by disease," which is repeated enough that I have a feeling looking over it may have changed the entire meaning of the song.

I agree with that mostly but I think its a broader thing, applying to more religions than just Christianity and Catholicism

The plague is my favorite song from As I Lay Dying.

"Reach out your hand. Reach out your hand, only to be plagued by disease." (this defines fallacy)

Just like the spread of disease(cancer:religion spreads rapidly and separate the good cells from the bad cells).... Ya... Ya... Debt and guilt or guilt and decree, the masters that we please.(Look at the intersection between 'guilt'. Either way we are screwed.) Yet if we seek help for infirmities, we are made twice the sons of hell as before.(If we show weakness then we are screwed even more)...