What do you mean it makes no sense, it's certainly convoluted but it does make sense. Bioshock exists in a multiverse, which is the theory of infinite universe's where anything that could happen did happen. In the universe of Biosock infinite Booker is a version of Comstock from another universe, one where he did not accept the baptism and thus never became Comstock, the Lutece's can manipulate the mutiverse and brought Booker to the same universe where Comstock exists so essentially you have the same person from two different universes in the same universe. The idea being the only person that could stop Comstock was himself.
"There's always a man, always a lighthouse, always a city." That is the only constant in the Bioshock universe, everything else is variable. At the last scene Elizabeth realizes this and decides to break the cycle, by removing hte man from the equation, so she drowns Booker who also realizes this and just lets it happen.
It's even more complicated than that once you get into the Lutece's roll in all this. Everything is their fault essentially, from my understanding.
Like I said it's very convoluted, but I think pretty creative and thought provoking when you fully understand it. Certainly MUCH better than Assassins Creed, I don't even consider that an opinion. AC is a load of dribble every time you're not in the Animus.