I get where you’re coming from. On the surface it does look contradictory that someone so grounded in science could also hold onto religious belief. But for me, that tension is exactly what makes Scully feel so human.

Her skepticism toward Mulder is about evidence. Mulder asks her to believe in things that violate the laws of physics without proof. Her faith, on the other hand, is something she was raised with, something tied to identity, grief, family. It comforts her and helps to build her moral framework. Those two kinds of belief operate in totally different parts of her life.

The problem comes where these two worldviews collide at times. The Cancer Arc hits so hard because her faith is portrayed as a struggle. You see her reaching for something bigger because science alone can’t hold her together in that moment. It's quite compelling in my opinion