Mulder was already an FBI agent (and searching for Samantha) before he believed that it was aliens that took her, right? If I recall correctly? Because he stumbled upon the x files and then underwent the regression hypnotherapy… I think… if that’s true I think it’s underemphasized that Mulder pursued a degree in psychology and was working in profiling/Violent Crimes trying to prevent what he went through from happening to someone else before he really ever had any leads on what happened to his sister.
The Man Who Searched for His Sister: Mythology and Motives
You hit the nail on the head to me.
From the Golden Boy of the FBI (revered, respected, and honored) to Spooky in the basement (a testament of "ego" and "self-destruction" to the mainstream), the fall from grace for Mulder had to have been a tough pill to swallow. As abrasive as he can be, he's also warm and fond and empathetic: more willing to make friends (Jerry Lamana, Reggie Perdue, Diana Fowley, TLG) than go it utterly alone. But after discovering the files in 1988 and finally reopening them in 1991, he begins to (rightfully) suspect interference; and, in the face of derision and rejection, withdraws. "You were sent to spy on me," he deduces of Scully in the Pilot; and he's not wrong about the intent of her assignment, though he misjudges her motives along with it. More accurately: he offsets his interest in her work and mind by testing her upfront, unwilling to tie his loyalty to a wolf who intends to chew up the files and spit them out.
(As a side note: the story behind his and Scully's career path is so well done. Traumas in their childhood pushed Mulder and Scully to discover the truth for themselves-- be it in Oxford psychology or medical school morgues or FBI recruitment and field work-- and shaped their lives: both wanted answers to unanswered questions, hoping it would alleviate their personal struggles. Mulder's "You can deny all the things I've seen, all the things I've discovered. But not for much longer. Because too many people know what's happening out there and no one, no government agency, has jurisdiction over the truth" and Scully's "Nothing happens in contradiction to nature, only in contradiction to what we know of it. And that's a place to start. That's where the hope is" exemplify this. Their goals were fixed, their longing and struggles years in the making, before they'd begun navigating towards each other; but with each other they found their personal truths, and in each other they found "the" Truth.)
Samantha marked Mulder's life deeply and irrevocably when she vanished. His family fell apart; his life fell apart. And perhaps-- like many other lost souls-- he fastened onto psychology to understand what happened. And in seeking and becoming a source of help, he then latched onto the elusive "truth" as the ultimate solution-- a vision, as The X-Files would call it (his memories always did come back to him in visions)-- and became a crusader, willing to spend a lonely lifetime in the basement, on the road, on a cloistered couch while life on this planet passed him by.
Another thought: was Mulder's peg leg desire-- "If you have a peg leg or hooks for hands, you know, maybe it’s enough to simply carry on living. You know, bravely facing life with your disability. It's heroic just to survive. But without these things you're actually expected to make something of your life — achieve something, earn a raise, wear a necktie. So — so — so, if anything I'm actually the antithesis of Ahab, because if I did have a peg leg I'd quite possibly be more happy and more content and not feel the need to chase after these creatures of the unknown"-- formed before or after Samantha's disappearance? I'd say before: that it was part of his nature, like Scully's, to prove his pain to himself-- he externally, she internally. He lost his sister, she killed her rabbit; both were haunted by invisible scars that drove them ever onward. But while he could stop, finally, if he had a wound to point to (even die if his death had meaning), Scully couldn't (and avoided, and feared, a final end): legacy, she found in the morgue, is forged in life "on this planet", not in box scores or down endless roads or in running back to the past. "I've got things to prove-- but for my own reasons" and "If I quit now, they win" and "Mulder, get up. Get up and fight."
Another 'nother thought: CSM often put Mulder up on a cross, projecting his own "martyrdom" onto the other man-- a sinner purifying himself by piercing his sins into the flesh of the Lamb of God and slitting his throat. An allegory wholly unfitting to his megalomaniacal narrative: he sees himself as "God" (says so directly, post here) while failing to recognize that his motives are entirely selfish; and that his sacrificial son is hardly righteous or perfect-- that, in fact, his Christ-like figure isn't out to save the world. Mulder's fathers (canonically, both of them) pinned their agenda onto him when that was neither his goal nor his ideal from the start-- the world, "life on this planet" as a rule was furthest from his thoughts. His was a personally rewarding quest, with "selfish", not "altruistic", motives-- he wanted to find the Truth, and expose it; to search out mysteries with a baseball and sandwiches and a house like Home and his sister and his partner. And that simplicity of perspective gave him true insight, able to see through the net of lies Bill Mulder and the Consortium and Jeffrey Spender and Krycek and Marita and Skinner (and even Scully, at times) were caught in.
