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.
2. This marks the first time in the series when, after the opening theme plays, the end credit doesn't read: "The truth is out there." In this case, it reads: "Trust no one." This is a hat-tipper to those über-geeks (like the 14-year-old me) who would sit through each and every opening sequence just to see what Carter would spit out in that end credit line. It would change again, in subsequent seasons, much to our collective glee.
3. The flask in question contains medically proven extraterrestrial DNA, which Scully herself takes to the lab for testing and hears the results firsthand. Our most skeptical of characters is finally handed the proof (or the "truth"). And she's just rendered speechless. Who can blame her? There's a great exchange between her and Mulder, in which she apologizes for not believing him up to this point in the series. "For the first time in my life, I don't know what to believe," she says. Deep Throat later fills in Scully and Mulder about the alien-human hybrids, key subject matter in future seasons. In a telling sequence, too, Scully asks Deep Throat why he gave them "so little to go on in the beginning" and has let on so much now? In other words, Carter has been the puppeteer behind Deep Throat all along—this is a message directly to the audience.
4. This is the first time we see what will become the telltale sign of an extraterrestrial "hybrid" being in an X-Files episode—a humanoid that looks just like a regular person but has superhuman strength and bleeds green. (Fringe's parallel universe people would've never bled mercury without The X-Files.)
5. The Smoking Man appears to be at the forefront of everything bad that happens in the series—and as of yet, Mulder and Scully haven't connected the dots (or have any reason to suspect him). The smug son of a bitch will appear many, many more times going forward. At the tale end of the finale, Carter has the Smoking Man recreate one of the most iconic moments in film history on the small screen—much to the joy, I'm sure, of the geeky audience. If you haven't seen the episode, first watch the last five minutes of the Indiana Jones flick Raiders of the Lost Ark, then compare/contrast.
A whole lot of other great moments take place in this episode, which I urge each and every one of you to watch or rewatch. And this, the season-1 rewatch is officially complete. Look out for the kickoff of season 2 at a 'Freak near you.