The interesting thing in the game is that there are about two audio logs from Letuce that is integral to understanding hte story and I'm not sure they are easy to come by. I found them, but I think a lot of people missed them. (one of them I only found because I was lost...)
In the logs, Letuce states that she figured out a way to suspend an atom in the air. From that molecule she worked with an apple and from those results she figured out how to float columbia. From that work, she started figuring out quantum entanglement. The atoms she was working with, she found, existed in her dimension as well as in another dimension. By morse code, she began talking with someone manipulating the same atoms in another dimension. That person turned out to be a male version of herself. She became interested/obsessed with opening a hole so that she could bring her "brother" into her reality with her. Meanwhile, Comstock saw this as an opportunity to steal a baby from another dimensional version of himself. So male letuce contacted booker with the proposition of bringing him the girl and erasing his debt. Booker accepted and then immediately regretted it. He tried to get her back, but when he crashed the site where the transaction was taking place, comstock took the girl before he could grab her completely. As a result, elizabeth lost her finger. Because she was split between dimensions, she has the ability to open tears at will.
When Comstock produced a daughter, Lady Comstock resented the girl. Comstock, who never really thought it was his fault to begin with, faught constantly with his wife until one day he murdered her. He blamed the murder on Daisy Fitzroy, who just happened to be there, as an alibi. Soon he also had the Letuces murdered to cover up his growing list of crimes. Because the Letuces had existed between dimensions, though, an aspect of themselves remains between dimensions in a sort of limbo. It is from this limbo that they crash around on multiple dimensions and try to find a booker who is capable of overthrowing comstock. They seem to constantly be poking at reality to see what they can influence and what they can't. Their existence is somewhat like the film groundhog day. Some things they cannot change like the coin always landing up heads, but other things they can influence like giving booker the recharging shield.
Comstock needed Elizabeth because his ultimate ambition was always to destroy, somehow, the surface world and use Columbia as a new version of Noah's Ark. He saw Elizabeth destrying New York City, and his own death at the hands of Booker. That was sufficient for him, and that was the ending he was attempting to guide the world to throughout the entire game.
It's at this point that I lose the plot. Comstock's plan works and Booker is too late to save elizabeth. She's old and the damage is done. But she sends booker back in time with a note for young elizabeth. Booker goes back in time to save her and manages to do it. It's at this point that Elizabeth somehow, I have no idea how, gains some sort of cosmic awareness. SHe says she can see all the realities, but she also seems to be all knowing. She takes booker, not to another reality, but to a non-reality that is the nexus for all realities. In this non-reality Booker sees other Elizabeth's doing the same spirit guide routine for other Bookers. Ultimately, and I feel like this is where the plot falls apart, she takes him to the spot where he was baptised and became Comstock, but NOT the same place. (there was a crown when Booker was baptized. Now there is nobody. Even teh preacher suddenly dissapears and leaves the other elizabeth's to drown booker.)
Personally, I wonder if the ending is supposed to branch into a spirit realm to make a point that there is some religion in the world of bioshock. It's not all strictly guided by science.
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