Lyric discussion by RockXWL 

Cover art for Mother Superior lyrics by Coheed and Cambria

I think this song is a discussion between Claudio and "Mother Superior (MS)." It could be Mariah, the ghost of Amebellina or even God (I've always been pretty sure that God in this story is a real person rather than a divine being).

"You'll just say the worst of me, with a hope they'll understand. No, they know you're just a boy, so grow up and be a man.

Little baby, kicking, you scream and whine. Victims pay the price eventually. The cost, let's see... your life."

I think this whole part is MS explaining to Claudio, "look, you are just a boy. It's not fair for you to have all this responsibility placed on you, but guess what? It is. And you've know about this for a while now so it's about time you stop whining and just deal with it." She explains that she knows that completing his mission will probably cost him his life but she tells Claudio to just deal with it, no matter how unfair it may seem.

"You've got nothing to prove. Stay afraid, young brother. You've got nothing to prove."

MS saying to Claudio there's no shame in being afraid - you don't have to prove yourself a man by pretending now to be frightened by the situation you find yourself in.

"Mother Superior, come catch the rabbit, he runs."

Claudio asking MS, "I'm afraid and I want to run away and forsake my responsibilities...convince me not to run"

"My, how've you been? You're frightened of leaving this truly gone fishing amalgam. Go fetch your gun."

MS replying to Claudio, "You're frightened but that's OK. Now go fuck people up."

So yeah that's my interpretation of at least some of the lines. I'm extremely interested in hearing other people's interpretations too.