Lyric discussion by foxxycotton 

I agree with sicanonym. I also think it's about corruption in the catholic religion. The pope is calling a rat something else. Rat as in a sneaky, lying, dirty person. "We'll call it all forgotten when we're done."

Meaning, we'll look the other way I guess. We'll call rats something else because the pope allowed it, and we'll just forget about it.

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