Dewitt makes a choice to either accept or refuse baptism after the battle at Wounded Knee
In one universe he refuses, becomes a pinkerton who sells his daughter, and leads the Vox Populi rebellion to a bloody victory over Comstock
In another he accepts baptism, changes his name to Zachary Hale Comstock, and teams up with the female scientist to create Columbia
Due to heavy experimentation Comstock becomes infertile and is unable to have kids
With help of the female scientist, Comstock then makes a deal with (the still fertile) Dewitt from the other universe to get a biological daughter. (In Dewitt’s universe the scientists was born a male and the two scientists get together as “twins” after the ability to link universes is learned)
At the last second Dewitt changes his mind and tries to call off the deal, resulting in baby Elizabeth (or or “Anna” as in Anna Dewitt: AD) losing part of her finger in a portal tear during the exchange (this also gives rise to her powers)
In order to hide the truth Comstock has the twins killed with their own portal machine in a way that makes it look like an accident
The twins are then scattered throughout the “multiverse”
The twin brother regrets his actions and convinces his sister to take Booker to the Columbia universe in order for Booker to reclaim his daughter and for the twins to right their wrong
In the process of crossing universes Booker forgets who he is and creates false memories of his purpose: “bring us the girl, and wipe away the debt”
So in order to stop the loop and the Columbia events in ALL universes, Dewitt must be killed before he makes the choice of baptism. This way he cannot become either Comstock or Booker--- which also means that the events of Bioshock infinite never happened, and that Elizabeth didn’t drown Dewitt. The end result would most likely be the scene shown after the credits.
• The booker we play is probably the 122nd booker, this can be seen in the coin flip results and the code to start the jet in order to get into Columbia in the beginning is 1-2-2
• The reference to the original Bioshock near the end could be that Bioshock is perhaps one of the alternate outcomes: Dewitt becomes both Atlas and Ryan.