"Rotten Town" is from the point of view of the pirate's ship.
The mutineers are plotting against the captain as I'm rotting in the goo
- Although now reading the lyrics, it's probably not since the narrator talks about stumbling down the harbor, not still looking... or whatever it was I though he said.
The boy in "Save Our City" grows up to be King Simius in "The Lamb and the Dragon".
A theory proposed in this tumblr post
suggests that the boy in "Save Our City" is actually the mayor's son. The mayor becomes increasingly delusional psychotic as the beginning of the end of the world approaches. Just before he commits suicide, he cries "Long live King Simius!" as a parting farewell to his son. Not only does it drive home the truth of his insanity... it turns out to be a sort of self-driving prophecy. Simius had previously demonstrated some measure of faith in God, and clung desperately to this faith after his father's death in an attempt to rally the citizens against the oncoming zombie hoard. However, as the end of the song implies, the entire city is destroyed anyway. Only a handful of citizens survive, including Simius — however, he is badly injured in the process, and receives a particularly bad wound to the neck. His injury, combined with the trauma of his father's suicide and the destruction of the entire city under his command, causes Simius to finally snap. He becomes hardened and blames God for abandoning him in his time of need. Years later, he becomes the leader of the rebel soldiers mentioned in the second verse of "The Lamb and the Dragon".