Lyric discussion by k3no 

Cover art for Mother Superior lyrics by Coheed and Cambria

i think its about Claudio reflecting on all of his bitching and whining he did throughout the story, and he finally realizes that the only way out is to become the crowing to set everything right.

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

Damn I love that part!