It's a long post, trust me, I know, but I think that it points out a few issues that are worth considering regarding the whole plot, philosophy and physics of the game and it's good to be read,Also, if someone has an explanation, I would be more than delighted to read about it.
One can grasp the sense of many of the things in the game , but there are still a few loose ends.
- Firstly, which Booker is drowned? If it's the version of Booker that the player controls (the version of Booker that gets to the end of things, instead of getting killed and failing), than the drowning is pointless, since it's a Booker who already made a decision, it's a future Booker, one who already passed the moment of the decision regarding the baptism. Killing a future Booker won't change the past, it's the other way around, isn't it? And the game shows us the Booker we control is the one getting drowned. BUT if SOMEHOW the past Booker (the Booker at the precise moment of the decision, since we can see Elizabeth being able to travel through time, not just through space) is drowned, than this is also illogical, since the Booker from that moment (the moment prior the baptism), won't know about all the stuff you learn throughout the game, since they haven't happened yet, have they?
- Furthermore, if we are able to set the above issue aside, there is the question of the moment of the drowning. Does it take place before the choice is even made, preventing there to be both Booker and Comstok or does it happen after he accepts the baptism, thus his drowning resulting in only Comstok being killed? If we accept the first explanation, than it means that not only Comstok, but the Booker who has Anna and sell her and etc. ceases to ever exist. This would seem to make sense the most, but then again, what of the last scene where Booker wakes up in the apartment with Anna being in her crib? If Booker is killed before the moment of choosing (whether to take or refuse the baptism), than the last scene could not possibly take place after the drowning . But if we accept that he is drowned after choosing to go through with the baptism, than Elizabeth's line "You should be drowned before the choosing takes place, before Comstok is ever born (paraphrased)", (which indicates that he is killed before he can ever make the decision) is the one who cancels out our choise or it's misplaced/misused. Also, being drowned after accepting the baptism, doesn't cut off all the branches, so there is no possible way that every version of Comstok is dead (and Elizabeth specifies that by this, Comstok ceases to exist everywhere).
- The next issue is this: Booker chooses to let Elizabeth drown him. But since it's a choice, than, accordingly with the multiverse theory in the game, another universe is created where he refuses to be killed. Thus, even if Booker is drowned in one universe (before or after the choosing) there is another universes where Comstok continues to exist, since Booker refused the drowning. This means that not all Comstoks disappear, but still Elizabeth states as a fact that with the drowning being initiated ALL Comstoks cease to exist. The two possible ways this can be discarded are the following: 1. since parallel universes are created by one choosing something, the only way an alternate-universe-where-Booker-refuses-the-drowning is NOT created is if there is no moment of choosing (whether to accept or refuse the drowning) AT ALL. And a moment of choosing is created when one is feeling uncertain whether one wants something or not. This would imply that Booker never even contemplated the possibility of refusing the drowning and he never ever wanted to avoid it, thus stopping a moment of choosing to take place (logically preventing the alternate universe of being created). OR 2. The above is bullshit, but rather Elizabeth is omnipotent which allows her to put a stop of the creation of whichever universe she wishes.
- Another issue is connected with Elizabeth's statement while they go through Booker's past: they cannot alter things that already happened, they can only revisit and watch. Than how the hell can she drown him IN THE PAST (since it is a fact that they go back in time so he can get killed)? If your first answer is she's omnipotent, than what is the need of that line?
- And the issue of all which shows that there is is prevented from existing by Booker getting drowned (which is what Elizabeth states AS A FACT): There are a lot of moments in one's life where one makes a choice (initiating the creation of alternate universes). Many of them are so insignificant (like choosing to go to the bathroom first and than to the kitchen, instead of the other way around) that they do not make changes in one's life (but do end up creating new universes). This would lead to the existence of infinite Bookers who will eventually end up choosing or refusing the baptism. But every one of them is part of a different branch, so drowning one Booker will kill of only certain Comsoks, but not EVERY Comstok, as Elizabeth suggests (since many of those universes are linked by a choice other that the baptism one). Thus there are still infinite number of Comstoks alive at the end of the game. What's more intriguing are the Luteces. They keep repeating the cycle of bringing a Booker to the Columbia universe to save Elizabeth and to get drowned at the end. But some of them ought to have failed (get killed somewhere along the way), which will leave many universes without a Booker to save Elizabeth, get drowned and kill a bunch of Comstoks along with him. And those Bookers cannot be replaced since every Booker that does reach the end gets drowned, thus killed. But there are also (accordingly to the multiverse theory) infinite number of Lutece pairs who initiate the cycle again and again, just like the pair Rosalind and Robert we get to meet during the gameplay. This only leads to the conclusion, that because of the infinite number of possibilities, there can't be put a stop to the existence of Comstok, which is what Rosalind is trying to tell Robert all the time: "Once things are set in motion, they cannot be stopped". She's not a fatalist, she merely understands the concept of the multiverse better than Robert himself does. Even the game's name allude to this fact- So the cycle the Luteces start over and over in order to prevent Comstok from ever existing can never end and history will repeat itself forevermore - Lives, lived, will live; Dies, died, will die.
There will always be Bookers and Comstoks who die, who died and will continue to die for eternity and Luteces who will try to right their wrongs. There will always be the cycle, the infinite loop.