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In regard to when Daisy Fitzroy threatens to kill the child in the Finktown level, she states that you have to kill the Founders at their roots or else they just grow back. Could this be a reference to the end of the game where Booker realises that the only way to kill Comstock is by killing him/self before the events of the story even started? If he doesn't, then Comstock would continue to exist in other alternate dimensions and therefore, not be defeated. For example, if Booker had just killed Comstock in the fountain when he confronted him, it would create an alternate universe where Booker decided not to kill him, and therefore Comstock could still win in an alternate timeline.
An often overlooked though important theme of the narrative is the concept of grace, particularly as articulated by twentieth century Christian theologian Dietrich Bonhoeffer.note (A German priest who spent time studying for his pastorship in the U.S., and would go on to write The Cost of Discipleship. He was a vocal opponent of the Nazi regime and ended up dying in a concentration camp twenty-eight days before Germany's surrender.) Bonhoeffer saw two approaches to finding grace, one of which he dubbed "cheap grace" and the other "costly grace". To him, cheap grace was the idea of dealing with transgressions one would feel guilty about by appealing to God for forgiveness, feeling forgiven, and continuing to transgress while secure in the feeling that they are still righteous and godly. By contrast, he thought of costly grace as something that takes a toll on its seeker, being a transformative thing in which the transgressor becomes The Atoner and seeks to make themselves a better person to address past grievances and genuinely works to find forgiveness rather than just feeling content that God forgives them. This is reflected out in the forms of Comstock and Booker as Shadow Archetypes of one another, with Comstock representing cheap grace and Booker representing costly grace. Both men have done horrible things that they are not proud of and sought to escape from. Comstock took the route of cheap grace, assuming that anything can be forgiven if one simply loves God enough and is loved by God in turn. This allows him to continue to do horrible things, secure in the knowledge that no matter how bad he is, he is still righteous and God forgives him. By contrast, Booker took the route of costly grace, and he has suffered greatly for it. However, despite that suffering he genuinely did (eventually) become a better person for it, and sought to make up for what he did and right the wrongs he has inflicted, though he has never really forgiven himself.