12. So she does some time lord god magic and merges all timelines into their origin point at the baptism, and drowns Booker, preventing him from ever becoming Comstock and eliminating all relevant realities
Ahh! This has been confusing me since I finished the game earlier today. I was wondering how drowning Booker would affect all the other timelines, but now realizing she has the ability to merge possible worlds makes it all make sense now.
It's not that she really merges them. She modifies the entire "Booker gets baptized" branch into "Booker gets baptized and dies in the process", which kills that entire reality. You must remember that the multiplied realities result from the Luteces interfering and bringing the Pinkerton!Booker into the Comstock!Booker reality - he makes his choices there, he fails, they do it again.
I think I'm starting to get a clearer picture. Does this explain why a Pinkerton!Booker wakes up after the credits--because Elizabeth only eliminated the possible worlds where DeWitt accepted the baptism? Also, could you explain, or point me to an explanation of the different Elizabeth's at the end? Shouldn't there be a lot more of them?