One thing we are all expecting from BS2 is obviously the plot twist that suddenly changes how you view your character and those around him and would most likely change where you stand in the conflict.
Obviously the whole "turns out you're evil" twist has been done already.
My theory is simply this; at some point either just before or after you defeat the Big Sister you learn that she is in fact your daughter. Let me elaborate. Many of Rapture's families were heart-broken by the taking of their daughters for use in the Little Sister program. During this time you were the father of one of these girls that was taken away. Instead of falling into despair and suicide (the Lutz family) your character decided to take a more active approach into finding out what happened to his daughter. Hearing something about a program called fail-safe armored escorts and how it is somehow connected to the Little Sister program he decides to volunteer. You have no idea that being a volunteer means that you'll be turned into a mindless monster. During the transformation process all your memories of your life are wiped clean.
Before the eventual reveal there would be the same kind of foreboding messages of this truth like those in Bioshock 1 (ghosts in Eve's Apple, Audio diaries, Ryan's subtle hints). The kinds of hints that would seem unrelated, just another story of everyday people in Rapture and only after playing through the second time would you see the clues fit into place. Finding audio diaries of yourself talking about your progress in your search for your daughter; before the reveal this would mean nothing to you, just another tragic story of the poeple of Rapture.



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That would be a double twist. We assume "Big Daddy" has to be a male, but prototypes can vary quite a bit from the final product..... heh, heh

