This is exciting on its own as a mythology episode and cliffhanger, but more interesting in how it exemplifies the X-files template.
The idea for me is that Mulder is the viewer, the same as the viewers of the show: curious to know, idealistic, drawn to stories that reveal. He wants to see into a complex web and reveal fundamental truth, which mirrors our own experience. What narrative arises around him in the show, stories about aliens, monsters, spirits, mysterious biologies, is the sort of narrative he'd fantasize about, conjuring secrets to investigate. It arises because there is the desire for it, which is the cornerstone of film noir far more meaningful than the clothes and shadows falling a certain way.
In this episode Mulder is outright handed the most important documents he could ever hope for, the most secret stuff. It's funny that they're handed to him by a guy called 'The Thinker', an anarchist hacker with grunge-rock hair in his mid-20s, the type of guy who would be a viewer of the show then. Apparently, he merely stumbled onto them one day, which is another way of asserting the magical (adolescent) nature of the experience, which is penetrating the murky, shady world of adults in the name of truth.
More instances of this adolescent distortion of the world, the distortion as byproduct of looking:
He experiences irrational, absurd behaviour, which is later explained as being under the influence of hallucinogens.
His own father is in the know, revealed as a chief engineer of what the son is driven to tear down.
He is brought into contact with Indians who can unlock the secrets, elder guardians who can decode the narrative 'truth'.
So is it a wonder that every teenager on the planet loved the show? Alas, typical for the show, our own seeing is not allowed agency in the world to determine the truthfulness of different levels. In better hands, we'd have to decide for instance how much of Mulder's exchange with his father really did take place, knowing he was under the influence.