Our story begins with a young woman running through the woods in her pajamas. Look, I'm not judging, but I can't help but think that was impractical running wear. Whatever, she falls down, someone comes toward her, and they are enveloped in bright Alien LightTM. The next day, she's found dead, with two marks on her back.
Meanwhile, in D.C., baby-faced FBI Agent Dana Scully is asked to work with baby-faced FBI Agent Fox Mulder. Did I mention they're baby-faced? I don't remember them looking like that. I'm not sure I like this "growing up" thing. Of note is the mysterious Smoking Man. He smokes. Season 10 rumors say he has still not died of lung cancer.
Anyways, Mulder is a legend, not only because he is a good agent, but also because he's a bit obsessed with government and alien conspiracies. Because of this, he's been sent down to the basement where they keep the X-Files: unsolved cases that are really, really weird. Such as the case of Pajama Girl. It turns out, Karen Swenson was the fourth person in her graduating class to be found dead out in the woods. While the other victims didn't have the marks on their backs, it appears a different doctor examined Karen's body.
Strange things happen to them when they head out to Bellevue. Their plane encounters sudden turbulence. Their car stalls in the middle of the road, and Mulder apparently keeps spray paint in the trunk of the car so he can mark places like this, or something. At least he'll never be unprepared? I wonder what else he keeps in his trunk just in case.
Mulder arranges to have the third victim, Ray Soames, exhumed, despite the medical examiner's complaints. However, they discover a deformed body in the coffin. Scully, who has a medical degree, examines it, finding a metal implant within the nasal cavity. Mulder starts salivating worse than Giorgio Tsoukalos, and Scully's glasses are skeptical.
"I don't even want to hear the word alien while I'm wearing my Skeptical Glasses."
On their way back, their car stalls in the same place, and after a blinding flash of Alien LightTM Mulder discovers they have lost nine minutes-which Scully is skeptical of, despite looking at the clock.
"You're not even wearing your Skeptical Glasses!"
"BECAUSE IT'S RAINING"
"BECAUSE IT'S RAINING"
At their motel, Scully is preparing for a bath when she notices two marks on her back. Severely freaked out, she runs over to Mulder's room, in her bathrobe no less, and gives everyone and Mulder some fanservice, before he says they're mosquito bites. It's pretty clear he's lying, since they look nothing like mosquito bites and everything like the other marks. He then explains to Scully why he is so adamant about his beliefs: when he was a child, he remembered seeing a blinding light in his room, and his sister vanished that night.
Then, they receive an anonymous phone call! O'Dell is dead, hit while running into traffic! They visit the scene, and sure enough, she was on foot, no wheelchair in sight. And when they get back to their motel...
It is on fire. Along with their evidence. The medical examiner's daughter finds them in this state, and has a story for them: she has the marks on her back too, and she's found herself in the woods in the middle of the night several times. Her father shows up to take her away, but our heroes are undeterred.
Upon exhuming the other graves, they discover them empty. Mulder realizes that Billy must have taken them out to the woods. Skeptical Scully is Skeptical, but when they visit the hospital, they find dirt all over Billy's feet.
That night, they return to the woods, and find Billy crouched over Theresa, lifting her up as a blinding light begins. However, when it ends, they find the two as they were, unharmed. Billy is returned to his right mind. Later, he is put under hypnosis, and claims he and some of his classmates were abducted during a forest party after graduation. They were being tested, and those who failed the tests were killed. Scully gives her boss the metal implant, the only evidence they have left. But she finds out that their case files are missing. We end with Smoking Man locking everything away in a Super Secret Room in the Pentagon.
Government conspiracies single-handedly keep the filing box companies in business.
The pilot did a great job of setting up the story, and I love that the overall series arc began immediately. It's easy to see why it caught on so quickly, and has been so beloved.