During the battle to destroy the Cylon resurrection ship, Apollo has to eject.  When victory is won, Starbuck nervously awaits the signal from Adama to kill Cain.  When the signal doesn't come, Cain also backs down.  Baltar help Gina/Six escape and she later meets Cain in her quarters and kills her.  Apollo apologizes to Starbuck for not being there to watch her back and then tells her that he was hoping to die while he was adrift.