Regarding the climax of The Autopsy of Jane Doe:
Austin's father (Tommy) begged the witch to 'not hurt my son instead take my soul'. Of course the witch took his soul but why she kill his son?
Austin's father told her that he is innocent.
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It's deliberately unclear for shock value, but a couple of options:
It is not about how she takes souls. What people have done to Jane she does the same thing back to them. In this process she takes revenge. Every time she takes revenge she heals herself more. Tommy does most of the autopsy. Hence he receives most the pain back. Tommy only thinks he's making a deal with her. But then Austin did one bit of the autopsy on her - cutting her head open. Notice when Austin falls he breaks his skull and dies. Jane cannot be bargained with. She will keep taking her revenge until she is fully animated.. and maybe even after. For the entire order of what was done to Jane check this. It appears that the only person who might have survived is the girlfriend and her death might have been an illusion created only for Tommy and his son. The girlfriend didn't touch Jane so she is out of this revenge cycle.