Sisters Affect Ending
The decisions you make during the game concerning how you deal with the Little Sisters and the choice characters (Grace, Stanley, and Gil) affect various components of the final chapter, but the final ending cinematic is based entirely on your choice regarding the Little Sisters.
Good Ending: If you rescue all the Little Sisters you deal with, you get the good ending.
Bad Ending: If you harvest all the Little Sisters you deal with, you get the bad ending.
Choice Ending: If you harvest at least one Little Sister and rescue at least one Little Sister, you get the choice ending where you can determine your fate. Choose to die to get the ambiguous ending. Choose to live to get the bad ending.
Eleanor’s Behavior
You may not have realized it, but Eleanor was watching how you treated those Little Sisters and the choice characters. She was learning from you, Daddy. She wants to be just like you, and she will. Eleanor’s behavior—the way she treats Little Sisters and the comments she makes—change during the Inner Persephone portion of the game based on whether or not she is the good Eleanor (Savior) or bad Eleanor (Harvester).
Good Eleanor: If you rescue all the Little Sisters you deal with, you get the good Eleanor.
Bad Eleanor: If you harvest even one Little Sister, you get the bad Eleanor.
Sofia’s Fate
The fate of the game’s primary antagonist is left in the hands of Eleanor. Whether or not Eleanor decides to spare her mother’s life is determined by the choices you made concerning Grace, Stanley, and Gil.
At the Hands of Good Eleanor
If you spare all choice characters, Sofia lives.
If you spare at least one choice character, Sofia lives.
If you kill all three choice characters, Sofia dies.
At the Hands of Bad Eleanor
If you spare all choice characters, Sofia lives.
If you kill at least one choice character, Sofia dies.
If you kill all three choice characters, Sofia dies.
And then father, the rapture dream was over…
Eleanor’s speech to Subject Delta at the end of the game also changes depending on whether or not Sofia lives or dies at the hands of good or bad Eleanor.