As far as first-season finales go, at least for me, this one ranks at the top. It just takes great, suspenseful TV to the nth degree—to that cinematic level. The plot is nothing short of Sir Arthur Conan Doyle–esque. And X-Files mastermind Chris Carter ties it all up at the end with a big red bow on this holiday gift of an episode (that's a bit of a misnomer, I realize; the finale originally aired in mid-May 1994).
I'll break this episode down into its key moments, all of which point to future episodes, seasons, plots, themes and even the X-Files theatrical:
1. Deep Throat (Jerry Hardin) again contacts Mulder and leads him directly into that great government conspiracy plot line, which weaves its way in and out of the first season (and appears as early as the pilot). This sequence of events gets Mulder closer than he ever has been to the "truth," which he so desperately wants to learn. And by truth, I suppose it's greater than just new knowledge for Mulder at this point in his career. The seed, we know, was the abduction of his sister, Samantha, by what he believes were aliens.
1a) I will not give away what happens in the last few minutes of the episode, but consider it epic and Deep Throat related.