So I got this theory now, tell me if you agree. Sofia linked to the Nightfire Pirates who were cursed. Former members of the crew went and founded that weird church and started doing sacrifices to stave off the curse, this is where Madalyn and her brother from the last game come in.
One of the books mentions that the sacrifice needs to have black hair and be a virgin, which only kinda fits one girl, Alia. Her mother keeps pushing her to be sexually adventurous and Naomi is of native ancestry, the same people the pirates plundered. Which could mean she's the one who cast the curse in the first place and kept Alia hidden and pushed her to have sex so she would no longer be suitable as a sacrifice.
Alia's parents also died in strange circumstances leaving her an orphan, it could be they were running away to save her but got caught in their escape.