Songbird, a massive mechanical bird that protects Elizabeth and that can be summoned and controlled by a whistle-flute thing, always seems to intervene at the last moment and take Elizabeth from Booker. When Songbird does this near the end, Booker tries to rescue her. He hears, through mini-tears in the air, Elizabeth being tortured and brainwashed into becoming the heir to the throne that Comstock wanted her to be.
After going through a tear into another dimension, Booker discovers an old, frail Elizabeth looking out over a burning city. The chaos is her doing. She explains to Booker that this can never happen and gives him a piece of paper to give to the young Elizabeth. He then goes through another tear into a universe where Elizabeth is still being tortured and brainwashed. After rescuing her, he gives her the note. All seems well.
They go on to find Comstock. But after he (Comstock) tries to get Booker to explain why Elizabeth is missing her pinkie finger, Booker kills him, denying any knowledge of it. Elizabeth, however, knows Booker knows something, even if he doesn’t remember.
They attempt to escape, but they are attacked again — this time by loads of Vox. Elizabeth then realizes she can control Songbird by using the whistle. They use Songbird to help kill the remaining Vox. Afterward, Elizabeth gets Songbird to destroy the Siphon; the original source of her power and a device that forces her to remain within Columbia and stops her opening up another dimension to escape into.
After it is destroyed, Booker drops Songbird’s whistle because it becomes electrified, and he panics as Songbird rushes toward them, no doubt about to flatten them both. But Elizabeth opens up a tear into another world, allowing them to escape into a new world.
The world of Rapture.
As they wander through Rapture, they then leave through a lighthouse door and come into a huge, massive, open, infinite space full of neverending lighthouses.
This is where the explanations start.
Beacons to other worlds
Each lighthouse represents a world, a dimension. What are these dimensions? Well, they could be anything, worlds never even heard of, but they are also the outcome of every possible situation and choice.
So, for instance, if you decided to stay at home (and play Infinite) rather than go to work, another dimension would be created for where you didn’t stay home and you did go to work. A new world is created for everything that could have ever been.
We then learn by going through one of these lighthouses that after killing Native Americans at Wounded Knee, Booker got baptized to rid him of his sins. But he refused the baptism at the last moment and went on to live his life. Booker and Elizabeth move on to another lighthouse — to another thing that happened in Booker’s life.
We are now in Booker’s apartment, and there is Robert Lutece standing in the doorway. You hear a baby called Anna in one of the rooms, and after entering it, you see the very young child Anna in a cot. Booker frantically denies that the child ever existed, completely confused as to why this is happening. But to continue he must go through with the scene as it happened before. He hands his child over to Robert, who then leaves, saying something along the lines of “Mr. Comstock forgives your sins.” We then go to a scene where we see Comstock holding Booker’s daughter as he is about to go through a tear into another dimension (the dimension of Columbia). But Booker tries to stop him leaving, begging for his daughter back. Unfortunately, Comstock gets away — but he isn’t quick enough, and as the tear closes, Anna’s little finger gets caught in the closing tear is cut clean off.
It is now obvious that Elizabeth, previously called Anna, is Booker’s daughter.
Now this is where it gets a little confusing. Booker realizes that the Lutece twins, who aren’t actually twins but are versions of the same person from different dimensions who met each other, came to help him after Comstock betrayed them. They came to help Booker get his daughter back from Columbia.
They opened a tear and brought him into Columbia’s dimension. After bringing him through, Booker’s mind created new memories in place of the old ones. He created a new purpose for himself in this other world, and this purpose was what he wanted to do all along: find Anna/Elizabeth and get her back.
Unfortunately, it wasn’t as simple as that.
Before entering the final lighthouse, we hear Booker saying about how they will just go back and kill Comstock in his crib to prevent all this. That, however, actually means killing himself, as you’ll see in the next section.
Booker, who art thou?
When, in the original dimension, Booker rejected the baptism, another world was created in which he accepted it. This is the place they are in now. This is the world where he accepted the baptism.
After being baptised, what did this new, free-of-sin Booker do? He called himself Zachary Comstock and created a city in the sky called Columbia. He was born again — but this time an evil man.
To kill Comstock when he was born, Booker has to kill himself when he turned into Comstock. And that is at the place in another dimension where he accepted the baptism instead of rejecting it.
Lots of Elizabeths appear, and they proceed to drown Booker, presumably in the baptismal basin. After he dies, we see all of the Elizabeths disappear.
Now, this is the end. The credits roll from there. Or is it? There is more. I will go into this after explaining all of the above, though.