On the other hand, however, while Scully is often two steps behind, she is hardly a sideshow to Mulder's genius—she is, in fact, quite integral to it. For, it is her constant analytic counterpoint that keeps his head on straight—helps to keep him level and clear, forcing him to translate his wild creativity into rigorous rationality. In doing so, she very often saves him from being too trusting and too willing to believe. For example, she immediately spots the forged alien spaceship photograph leaked by Deep Throat, intended to throw Mulder off the trail of an alien autopsy—when Mulder would like nothing more than to believe he finally has proof positive of alien visitations to Earth. Nor is Scully's intelligence and value lost on Mulder: "As difficult and as frustrating as it's been sometimes," he tells her, "your goddamn strict rationalism and science have saved me a thousand times over. You kept me honest. You made me a whole person" (The X-Files: Fight the Future).
Mulder's right, and he recognizes in Scully what James sees in Clifford: the will to believe and extreme caution are equally integral to the discovery of truth. Indeed, there are, according to James, two goals of inquiry: one, to seek truth, and the other, to avoid error. Logically speaking, these should work together. But, in practice, they do not. Searching for new and creative hypotheses to explain strange phenomena is searching for truth. But worrying too much about mistakes, while we are brainstorming, will not help. That is the second stage, where we test hypotheses and examine empirical results.
And it is precisely here that Mulder, in his search for truth, needs Scully and her correction of error and extreme caution in the search for evidence. This cautious error correction helps Mulder refine his search, making him ever more systematic and careful in his analysis. At the same time, Scully gradually comes to see the limits of her own scientific methodology. While she never gives up on the scientific method, she does, however, come to expand her field of vision. She begins to open her paradigm to the things of Mulder's world, ultimately seeing with her own eyes hard evidence of the truth that Mulder has long known about aliens, conspiracy, and the end of the world. In fact, by the end of the series, after Mulder has been abducted by aliens, it is left to Scully to explain to Agent John Doggett (Robert Patrick)—someone just as skeptical as Scully used to be—that "Gibson Praise . . . is part alien" ("Without").
For the philosopher, this is the true arc of the story of The X-Files, un derlying the massive mythology plot of alien conspiracy, how two minds, one wild and creative, and the other empirical and analytic, are fused into one—into a "whole person," as Mulder puts it. Mulder sharpens his wild imagination on Scully's hard empirical method, while Scully opens her mind more and more to the various political and metaphysical possibilities at work behind the scenes. As this whole person emerges, moreover, a greater noir detective does, too—one who sees more and more deeply into the truth (as the seasons unfold), and the arc of the mythology reaches its climax. Yet, somehow, even this whole person must necessarily fall short of the task. For, with all their powers of mind and their mutual trust in one another, they are ultimately led to a place that neither expected, where even reason cannot help them. Indeed, here they come up against the very limits of their own methodologies, in the face of the greatest terror they can possibly imagine. And it is here where they must leave their abductive logic and intricate detective semiotics behind and embrace a strange kind of faith—though not for any of the reasons Scully used to hold, and despite all of Mulder's arguments against them. The aliens are coming, and there is absolutely nothing they can do—but hope (blindly) in what, they do not know.
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