The insanity really begins when a group of enemy soldiers, ordered to stand down by an authoritative disembodied voice, simply lay down their weapons, get on their knees and start praying. You don't have to kill them, but we did, and they didn't move a muscle as we systematically gunned them all down. What can we say?
The next scene plays out much like the first conversation with Andrew Ryan in the first BioShock. You enter a room, and a massive black and white screen in front of Booker lights up with Comstock's face. From their conversation, it's clear that Comstock knows way too much about Booker's past, and Booker starts to really wonder why he's there in the first place. It also becomes clear to the player that there's more to Booker that we've yet to discover by this point.
After evading an assault from Comstock's militarized zeppelin (epic), you'll board the airship and attempt to commandeer it. But in another display of blind religious zealotry, a child sacrifices himself to destroy the zeppelin and take Booker out. Yeah, Comstock is a dick.