The trouble is, we, the viewers, get a god's eye view of the action. We see that the monsters are real, and experience every magical moment of proof. Scully is a scientist plucked from our world and placed in Mulder's world of mystery. In our world, magic does not exist.

We experience weird and unexplained things all the time, and every single time there is a rational, scientific explanation for the evidence. UAPs actually are weather balloons and experimental aircraft. Mexican alien mummies are just plaster cast hoaxes. The guys who had a dead bigfoot in a cooler were lying for attention. Scully, in our world, would be correct every week, and we have a lot more Mulders than we care to think about.

Scully is a scientist. She does not dismiss that there are things we don't know. She dismisses the fantastical explanations presented without evidence, and we see week after week that Mulder doesn't have evidence. In the show, there are shadowy forces deliberately destroying evidence and disposing of bodies to keep secrets, always just outside Dana's peripheral vision. From our seats in front of the TV, we can see them, but she doesn't.

So when she sees something she cannot explain, she assumes that it is consistent with everything else she knows, everything we know in the real world. Fantastical experiences have natural, mundane explanations, even if we can't see them. Coincidence, hallucination, imagination, pareidolia, smoke and mirrors, misdirection, and hoaxes. If you see a magician pulls a rabbit from a hat, you may never know how he did it, but you don't assume martians created a wormhole in the hat and wear bunny costumes. That's what Mulder sounds like to Scully at first. It just so happens, in this show, that Mulder is dead on balls accurate.

Iirc it becomes progressively more obvious to her. Character development and audience relatability

literally sees a man go invisible and then gets choked by invisible man

"There's got to be a rational explanation!"

"Yeah, Scully, and I think the rational explanation is that he really can go fucking invisible!"

There's something to be said about the whole "wanting to believe" thing for Mulder. While Scully may be rational and skeptical, there may also be a part of her that "doesn't want to believe" something outlandish.

If so, both Mulder's and Scully's gut instincts are technically irrational (because it doesn't make sense to "want to" believe something or not), but hers has a lifetime of reinforcement that is hard to break, even for an otherwise rational person.

just been watching the first season of the x-files for the past few weeks

Oh boy do you have some fun coming up.

I see most of X-Files filmed from Mulder's POV. There are some filmed from Scully's POV and you understand why she doesn't believe Mulders theories.

S3A:E12 is a good one from Scully's POV

There's a fan theory (that became my headcanon as soon as I heard it) that the episodes we see are the minority of their cases that are actually supernatural. Most of their cases have mundane explanations so Scully is always skeptical because she's usually right.

Just because you had aliens last week doesn't mean that you can have Bigfoot this week. Blurry photos and poorly substantiated ravings don't become good evidence of things until you get a lot more genre savvy.

And just because the thing you have matches Bigfoot on points one, five, and six doesn't necessarily mean it's going to be like Bigfoot on points two through four. Especially if there's not a unifying theory of Bigfootness behind them and they're just a list of aforesaid poorly substantiated ravings.

The easiest answer is that the plot and themes required it. The same way horror movie victims do stupid things like splitting up or checking on noises in a dark basement. It's necessary to advance the plot or maintain the status quo of the character relationships. Mulder needed a foil to his eagerness to embrace aliens and conspiracies as the explanation.

I think you are right : in this universe and since her character is described as rational, because of all the evidence she should come to believe.

Now of course, from a scenarist's perspective, for the plot, it is necessary to have someone at the center which is forever skeptical and one who wants to believe.

Vince Gilligan also met Bryan Cranston on this episode. It's a good one btw.

They would later collaborate on a small time show.

Oh. And the stock radio chatter that is in every episode and sim city.

I'm showing my age.

Edit: found it 28 seconds in or so.

Edit 2: I'm watching the eve 6 one. They use it multiple times there.

Has the series aged well? I haven’t seen it yet, but wondered whether I would like it.

There's pretty good in-universe explanations that are probably more in line with what you wanted out of an answer but also, it's clear that it is because it is her role both literally within the FBI, but also for writing purposes, to be a foil to Fox Mulder.

It actually worked really well in the early episodes. A classic duality, characters of opposing extremes brought together. Dana continually see things that challenge her rationality and she has to grapple with that while maintaining what she sees as a duty to remain grounded and offer the possibility of the explainable amidst the seemingly inexplicable. The apparent erosion of this level-headed front in the face of the extraordinary and supernatural week after week was initially a point of interest and development in the show.

The problem is that this established the dynamic between Fox and Dana and it was that, that made the show great so they had to keep it up but as there seemed to be no over-arching multi season arc planned they had to keep this going long after it still made any sense. This is especially evident when you see that attempts were made to carry on whole season long arcs while at the same time keeping the Monster of the Week episodes in between story episodes, so Dana would, in one week acknowledge her own direct personal experience and go all-in on taking down the conspiracy and seeing them aliens, and in another week somehow be totally skeptical of Fox's latest crazy supernatural crime solving theory as if it were the first season all over again.

Where are you watching these episodes at? I think I watched the first episode on some streaming service a long time ago, and never got around to watching the rest.