Elizabeth slowly and cautiously poked her head through the giant hole in the wall. She could see a long hallway to her right which led to some sort of viewing room. The far end was a gigantic glass wall which served as a massive window through which to view Rapture. The view of the underwater city was breathtakingly beautiful to her eyes.
Or rather, it would have been if that scumbag Atlas and his slack-jawed lackeys, who were standing in front of the window, were not obstructing the otherwise perfect view. Elizabeth sighed. She did not look forward to the upcoming confrontation, but she knew that it must come to pass, for Sally's sake. She wouldn't be able to live with herself if she abandoned the girl yet again, for Elizabeth had a debt to repay.
But some part of her was hesitant. It stopped her from stepping through the tear in the wall and proceeding down the hallway. Perhaps it was the part of her mind that summoned the auditory hallucinations of Booker speaking to her. "Booker" had repeatedly reminded her that Atlas most likely planned to kill her instead of holding up his end of the bargain. She knew this to be true, and fought against her self-preservation instinct. It was worth sacrificing her life to rescue Sally, she told herself.
Just as the former tear-opening lady was about to step through, a though occurred to her. If I'm dead, what reason does Atlas have to let Sally go? He'll just harvest her for ADAM anyway. It seemed like a reasonable conclusion. Elizabeth knew the implication was that her sacrifice would be meaningless. As she furrowed her brow, pondering what do, another thought occurred to her. Why don't I just take Sally from him? She faceplamed herself after she thought this. How could she have been so stupid and forgotten that she had plasmids, vigors, and stealth? After all, Atlas had taken her weapons away, but it was impossible to take away vigors and plasmids. Elizabeth's cheeks flushed red with embarrassment at herself.
"Hey boss, when is that lady gonna be gettin' here with that ace in the hole thing you wanted?" one of Atlas' minion piped up, disturbing the silence in the cold room.
"I can tell you one thing, if she doesn't get here quickly, Sally here is going to suffer for it." Atlas stated, elicting a laugh from the majority of his lackeys. The laugh was cut short when Elizabeth seemingly stepped into the room from out of nowhere. None of the men in the room could recall seeing her approach from the hallway.
Before anyone could react, Elizabeth seemingly threw some sort of snowball at the men. They instantly became columns of ice, incased in inches of thick frost. They were bunched pretty close together, so it took a couple of throws of Old Man Winter to freeze them all.
After the deed was done, Elizabeth quickly ran over to Sally and took her hand, dropping the code for "Would you kindly?" in the process. After all, she had no idea what it was and she did not care. All she cared about was Sally. "We need to get out of here. You're safe now Sally, follow me." Elizabeth said.
It took a little more convincing, but Sally eventually went with the pretty lady. The men would thaw out for sure, but it would take too long. By then, Elizabeth and Sally would be long gone, waiting until the building rose up to the level of the rest of the city, and then hopping over to the rest of Rapture.
Atlas wouldn't have time to pursue them. Unbeknownst to Elizabeth, Atlas would find the code she dropped and have way too much on his plate with manipulating Jack. He wouldn't be able to worry about some random, unimportant lab assistant. And as for Sally, well, there were lots of other little girls whose ADAM Atlas and his men could take.
Author Notes:
I decided to write this because I was really frustrated with Burial At Sea Episode 2's ending. Elizabeth's sacrifice is completely pointless, and logically it shouldn't have worked. It makes absolutely no sense for Atlas/Fontaine to let Sally go after he kills Elizabeth. Atlas easily could have harvested Sally anyway. The writers also failed to explain exactly how Elizabeth lost her plasmids/vigors, so I'm assuming she didn't. As far as I know, taking a person's plasmids/vigors away is not possible. Thus, I don't see any reason why Elizabeth can't rescue Sally and both characters survive.
Of course, I'm also completely disappointed that none of our questions about Burial at Sea's events or the leftover questions from Infinite were answered. That said, since Elizabeth lives at the end of this story, you as the reader can imagine that she probably would have discovered those answers, given enough time. It isn't perfect, but it's the best I can do. I have heard about a dozen fan theories to explain the massive amount of loose ends and plot holes, however none of them are explicitly stated or even implied in game. If it didn't come from the game, it's just a wild theory with no support.