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Why would songbird capture our Elizabeth in the 2nd parallel universe when the Elizabeth of that universe was never saved by Booker (he died a martyr before he could reach her)? Was it simply because songbird happen to chance upon her? Also, shouldn't that universe now have two Elizabeths (this wasn't reflected in the game)?

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Maybe she somehow escaped? Maybe by opening a tear, both versions merge into one (explaining why they remember things from both worlds at once and start bleeding by the nose). – Nolonar Apr 23 '13 at 7:09
@Nolonar: In that case, shouldn't Booker and Comstock have merged as well? Or do the Luteces' tears work differently from Elizabeth's? – hammar Apr 23 '13 at 13:13
@hammar Ah, I forgot about Comstock... Anyway, whenever it's about travelling through time or parallel dimensions, stories tend to develop major plot holes (mainly because we don't actually know what is supposed to happen when people travel through those). I assume Bioshock Infinite is no different. – Nolonar Apr 23 '13 at 13:54

My understanding is that Booker and Elizabeth don't actually travel between the dimensions. Elizabeth creates a superposition of two (or more) universes instead.

This is consistent with how tears work during the combat, how the Siren is brought to (un)life and explains why the guards in the club remember being dead.

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If that is the case then there wouldn't have been a Booker that died a martyr in one of the other universes now would there? I believe this is just a major oversight from the part of the developer which I can't blame them for as such a paradox was bound to happen one way or another. – Presanth Michael Apr 24 '13 at 4:11
@PresanthMichael: Alternate Booker dies before the merge of two universes, just like the guards or Chen Lin, so I don't see a contradiction. – mostlyautumn Apr 24 '13 at 6:51
@mostlyautumn Comstock + Booker + merging-theory == Paradox – Nolonar Apr 24 '13 at 8:18
@Nolonar Booker was brought by Luteces, not by Elizabeth. Anna and Robert went through a portal created by Lutece machine that looked like a hole you step though. When Elizabeth opens a tear e.g. in the interrogation room, you stand still while the world around changes. I agree it's a flimsy explanation but it works for me. – mostlyautumn Apr 24 '13 at 10:24

Needless to say, SPOILERS!

"Whenever Elizabeth opens a tear, she is moving to a universe that contains the conditions that she wants or needs at the moment. However, her ability also has a small area of effect, bringing with her people around her in a small radius. We can see this shown when Fink's Head of Security is unaffected, despite being dead in the first timeline. Whenever a tear is opened and the people step through, the mind will attempt to settle paradoxes by rewriting memories.

The first paradox we see is the state of being alive or dead, which affects Chen Lin, Booker, Lady Comstock, and two guards. What happens here is that the memories of the dead and the living are in conflict with each other, so the mind will attempt to combine memories of death with life. The effects of this seem to vary in intensity and results. A common ailment is that people will end up feeling traumatized and deeply disoriented, often seen struggling with their deaths. A possibly more intense reaction is the formation of new abilities, although Lady Comstock's situation is a bit special as 1) Elizabeth's powers were forced by the Siphon and 2) the Lady Comstock brought over is the one that encompasses the traits that Elizabeth imagined her to have .

Booker's situation is a special case as he is actually stepping into another universe. Thus the memories that merge will collect in his mind, which is seen in the case where Booker has memories of leading the Vox revolution. What is interesting is how Booker is unaffected when he's jumping from the first to second timeline in The Good Time Club. My guess is that because Booker is stepping into a timeline where there isn't a Booker. However, because the circumstances would've been the same, the mind does not have to rewrite his memories. This idea is tenuous at best, and could simply be the result of an oversight by the developers unless someone can explain this better.

The second paradox is the state of existing or not existing in the timeline, which is what affects Booker and Robert Lutece. Because Booker steps into a timeline where he doesn't exist, Booker's mind is trying its best to rectify that, muddling his memories to fit within this new universe. Robert Lutece also experiences this as well when he crosses over to meet his sister. This is a type of paradox where the memories of the same people will not merge.

Why is it the second paradox people will merge, but not the first type? Well, I can theorize that it has to do with whether or not the memories merging belongs to the same people. The Chen Lin in the first and second universes have the same identity and are practically similar, so their memories will merge. However, Booker, Comstock, Rosalind, and Robert are largely unaffected by the paradox of being in two places at once, with some minor hemorrhaging on the side of Booker and Robert. This may be due to the fact that there is enough of a difference between them that the universe allows them to exist simultaneously. In the case of the Lutece twins, what separates them is their gender, where combining them would probably induce another paradox of being both male and female. For Booker and Comstock, it is mentioned that Comstock's own identity has been eroded due to repeated exposure to the tears, thus making his identity different to that of Booker's.

So, what about Elizabeth? Why is she not affected in any way? Again, we have a special case where Elizabeth's power over the tears allow her to retain her identity and memory. We cannot say for sure, as the origin of Elizabeth's powers is simply explained with a hand wave of being in two places at once*, and the game doesn't delve deeply into this."

Source: Reddit /r/BioShock post, "Bioshock Infinite: The Ultimate Spoiler FAQ", by Reddit user awchern
If basing on the BioShock Infinite timeline suggested here (Imgur mirror), we can see that there was a multiverse "branch" after the event where Elizabeth was captured by Songbird: one where Booker failed to rescue Elizabeth, and another one where Booker successfully rescued Elizabeth.

Songbird had already captured Elizabeth in both universes. The main difference between the two was whether Booker was successful in the rescue attempt. There wasn't an instance of two Elizabeths in the universe where Booker rescued Elizabeth.

* More info at: Where does Elizabeth get her powers from?
† Source: "Attempt at a BioShock Infinite Timeline" post at the Reddit /r/BioShock subreddit by Reddit user, haettenschweiler

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