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In an episode of Doctor Who, Donna is skeptical about a murder mystery revolving around Agatha Christie. She states, "A murder mystery involving Agatha Christie is like Charles Dickens being surrounded by ghosts" (Which happened in an earlier episode)
I think they actually did that one in reverse in that episode, or the Shakespeare + Witches one, but it's been a bit.
one question..how can we have a skeptic in a sci-fi/horror/fantasy story and avoid both this trope and Arbitrary Skepticism?....serious question?
If Jesus, Then Aliens is the situation you describe. In a world of magic, Jesus could simply have been a wizard. So one who doesn't believe that Jesus existed (despite being seen) would be Arbitrary Skepticism. But the skepticism towards him being the son of God would not be arbitrary because (as I said) Jesus could have been a wizard.
Does that make sense?
Or in a similar vein, you could have a world where magic is real, but have certain characters doubt that there are gods. The priests claiming to use divine powers sent from the gods may only be using a different form of magic.
Or have a world with "gods", but have your character doubt their actual divinity (maybe they're just very advanced extraterrestrials).
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How well does it match the trope?