Until Season 3, for all his manly bravado and brave intensity, Fox Mulder retained something childlike about him. He had the clear-eyed purpose and moral clarity of someone who thought he knew something about monsters, about where they lived and what they wanted. Even at his lowest points, when his faith ebbed and he didn’t feel strong enough to search, his worldview remained remarkably consistent. Through most of Season 2, the truth seems fairly cut and dried: Extraterrestrial beings exist. They’ve visited us, but the government covers it up while tinkering with the alien technology and DNA. There be dragons, and Sir Foxalot was on a quest to slay them and save Princess Samantha.
In Season 3, Mulder learns that the real world rarely offers such simple truths.
For sheer X-Files-myth density, you just about can’t beat “The Blessing Way,” “Paper Clip,” “Nisei,” and “731,” so you might want to strap on your spelunking helmet before we get started. It gets dark and labyrinthine down there where “The X-Files” storyline grows up and starts getting good and complex.
Season 3 premiere “The Blessing Way” picks up where knuckle-whitening cliffhanger “Anasazi” left us. We think Mulder was burnt in the train car full of bodies. In reality, he hid, broken and dehydrated, under a pile of rocks until the Navajo rescued him. They take him into a special tent and perform the Blessing Way chant over him, whereupon Mulder’s recently murdered father arrives in a vision. He admits to having lied to his son in order cover a terrible truth that would have destroyed him, and he says that Mulder will uncover that truth if he goes forward.
While Mulder’s presumed dead and chilling in a spiritual teepee, Scully endures one of the worst weeks ever. She thinks her partner has died, and everyone assumes she has the digital tape containing the hacked files from “Anasazi.” She gets suspended for insubordination and finds out that she has a weird microchip embedded in her neck. This understandably freaks her out. Her sister Melissa convinces her to try hypnotism to recover memories from her abduction, an experience that does little to comfort her. To cap off her truly awesome couple of days, she finds out that the people who want the tape back are going to have her killed. She escapes, but Melissa gets shot and eventually dies, instead.
“The Blessing Way” segues into “Paper Clip.” Mulder and Scully learn that the United States government gave clemency to Nazi compatriots of the infamous Dr. Mengele. They hunt down one of those Nazis, Victor Klemper, who reveals that Mulder’s father was somehow involved with the human tests they performed. He also directs them to a huge cache of medical records and tissue samples. They find one file for Scully and another originally labeled Fox Mulder that was changed to be for Samantha instead. Suddenly, the lights go out. Creepy little bald guys run by Scully in the dark, and Mulder sees some kind of enormous, brightly lit craft take off.
They go back to keep questioning Klemper, only to find the so-called Well Manicured Man. He’s the super secret someone who earlier warned Scully that someone would try to kill her. He tells them Klemper is dead, and Mr. Mulder helped collect genetic data from the population in the service of creating an alien-human hybrid super race. He also says they took Samantha as insurance to keep Mr. Mulder from exposing the project.
Scully may not buy any of it, but Mulder feels he’s on to something. Convinced that the files contained records of alien abductions, and beginning to put the pieces together, Mulder confronts his mother. He asks if her husband ever asked her to choose between her children. Until this point, Mrs. Mulder had made an art of evading her son’s questions about his father’s past. Now, she admits that Mr. Mulder did, in fact, ask her to choose between her children, but that she was unable to do so and always hated him for it.
I think many adults can point to a moment when they suddenly realized their parents were just people, not superheroes, not a king and queen, but normal, flawed people. Once you realize that, the world loses some of its simplicity; if your parents aren’t what you thought they were, what is? You grow up some in that moment, but you may never be as safe as you were before.
Mulder learns that his parents had secrets and told lies under some truly dramatic circumstances, and it shakes his foundations. It’s a turning point for both Mulder and the story he inhabits, a point after which neither the character nor the explanations the plot provides will seem so straightforward again. At the end of Season 2, I suspected everything would get wrapped up directly. A half-dozen episodes later, and I began to get an inkling of just how much I didn’t know.
There are a few great monster-of-the-weeks next, but I’m wired into myth-mode. I’ll talk about them next time, and just move on to season 3′s other one-two punch, “Nisei” and “731.” At this stage, the show either totally confirms or utterly undermines your theories on what’s going on, depending on who you believe. It begins when Mulder orders a seemingly silly alien autopsy video from an ad in a magazine and ends with Mulder and Scully’s beliefs farther apart than ever.
Through the decidedly convoluted process of investigating the video’s origin, Mulder and Scully learn a few things. The Japanese, in addition to the Nazis, were brought into the United States to perform all manner of unpleasant tests on human subjects, and a secret railway exists to ferry the subjects around. They also hear about a lady named Betsy Hagopian who seems connected with the business in ways they can’t yet fathom.
Mulder goes to check out the trains while Scully looks for Betsy. She finds out that Betsy is in the hospital with terminal cancer. She belongs to a group called the Mutual UFO Network, or MUFON. The MUFON women think Scully looks awfully familiar, and they all have a neck chip just like hers. They say that Scully, like all of them, was abducted, and they’ve got the scars and memories to prove it. Whether she likes it or not, Scully begins to get back more of her own memories, and she reluctantly begins to lend credence to the abduction theory.
Meanwhile, Mulder goes sort of Jack Bauer and sneaks onto a train with a thing that resembles the bald dudes that ran past Scully in the records cache. He’s convinced he’s found some kind of extraterrestrial biological entity. Before he can get a good look, a Japanese scientist gets killed and an NSA guy shows up. Mulder, the alien thing, and Mr. NSA end up locked in the train car in the middle of nowhere with a bomb ticking down before a timely appearance by X saves the day.
Scully follows an evidence trail to a leper colony/ experimentation facility/death camp that leads her to a different conclusion. A shadowy member of the conspiracy, known to fans as The Fat Man, shows her a train car identical to the one in the alien autopsy video. She recognizes it as the one she was taken to during her abduction. He plays on her continuing suspicions about the unexplained, and convinces her the whole alien hooey functions as a smokescreen.
She tries to convince Mulder that it serves to cover up the real crime, namely, that the US government performed nuclear and biological tests on its citizens. By proselytizing for the lie, she believes, Mulder does the work of hiding the truth for them.
Of course, Scully’s right and she’s wrong, but we didn’t know that at the time. I recall thinking it seemed unlikely that a sort of mega-Tuskegee experiment could explain everything I’d seen. However, the baddies did such a lovely job hiding one big lie in a tapestry of near truths, I couldn’t completely deny that explanation either. Scully could believe that because abductions aren’t what she thought they were, that means there aren’t such things as aliens. She never wanted Mulder to be right in the first place, and after her abduction, it became even easier to accept any explanation less disturbing than being taken away in a flying saucer and probed.
Mulder isn’t sold; his childlike moral clarity has been shaken by the events of the first half of season, but he that doesn’t mean he can accept something quite so mundanely evil. At the same time, the things revealed in “Nisei” and “731″ make it pretty darn clear to the audience that whatever the truth turns out to be, it’s more complicated than the fairy tale he so wanted to believe.