Written by Chris Carter
Directed by R.W. Goodwin
With no one connected with the show knowing if there would be another season, Chris Carter decided to go for broke and write the Season 1 Finale as if this was it. In doing so, he gives the conspiracy that has been floating around since the Pilot depth and a purpose, and simultaneously seems to build up and tear down the foundation of The X-Files. This becomes clear in the opening credits when the message is changed from 'The Truth is Out There' to 'Trust No One'. Eventually fans of the series will come to look for these kinds of messages in the credits, but seeing it for the first time, it makes everything seem unstable.
Mulder and Scully are finally given direction and purpose from the mysterious informant that only now Scully gives any kind of identity to. The very fact that both agents have become as frustrated with the character as so much of the loyal audience must have been at this point finally seems to give Jerry Hardin some direction for his character as well. He doesn't seem like some avuncular hanger-on; he comes off as someone who is fully angered by what's happening, and afraid of what might happen if he dares to expose himself any further--- desperation that is proven all too vital by what happens in the story.
As if admitting the flaws in keeping everything vague up until this point, The Erlenmeyer Flask seems to be worth it's weight when it comes to revelation. Watching the episode with nearly two decades between it, one can't but help but wince a little at some of the unsayable dialogue that Carter gives so many of his characters, as if that's the only way to give weight to the unimaginable. After months of chasing their tails, Mulder and Scully finally seem to find proof that their work has not been for nothing ---- a flask containing bacteria that can only be described as extraterrestrial, men being held in tanks as if they were so much tropical fish, and as ff to be handed the golden ticket, an alien fetus that seems to be the wellspring of everything they've been chasing. Now that they finally seem to have the truth within their grasp, the depths of what they've been chasing seems to reveal itself as stark and frightening.
Of course, the operative word is 'seems'. As will become the case with almost every major element of 'the mythology', the truth is held in reach of Mulder and Scully before it is completely yanked away. Even at this relatively early stage, Carter and his colleagues seem determined to make sure that every potential world changing reveal is immediately snatched out of our heroes grasp after the audience but not the rest of the world can see it. What makes it seem so much more effective this time is that there actually seem to be consequences for all of this. The scientist who reveals to Scully genomes with what appears to be alien DNA is killed, along with her entire family. The test subjects Mulder glimpsed are so quickly referred to as being disposed of, we barely even register that they've been killed. And in conjunction with all this, it's revealed that the protagonists are helpless before these large events--- Mulder can barely offer protection to Secare before he is murdered in front of him, Scully insists on making the trade for Mulder's life only to have Deep Throat insist on otherwise--- and being almost casually executed as it happens. The death of Deep Throat comes as a real shocker too---- his insistence that he is risking far worse things than exposure is finally, fatally justified. And as a final act, the X-Files themselves are shut down, with our heroes powerless to stop that either. Even Mulder's last lines of perseverance seem utterly futile before the final scene--- written out to mirror that of the Pilot--- when the Smoking Man takes the evidence that blood was shed for, and files it away among hundreds of others. Their hopes seem utterly and completely irrelevant beyond the powers that be.
The X-Files has spent it's inaugural season, like so many series, before it struggling to find it's identity. It has tried to be a series dealing with the paranormal and the supernatural in a methodical, realistic way. It hasn't helped matters by the fact that Carter seems only occasionally able to grasp the idea of what his series wants to say. Morgan & Wong seem to have a clearer picture of what the series can be whenever they are granted access to it, but the shows founder doesn't seem quite as able. Decades after the fact, with Mulder and Scully iconic characters, it's hard to believe that Anderson and Duchovny don't seem to have a handle on it yet, though Duchovny seems to be a lot closer to it in the latter half. All of this would seem to irrelevant because at this point in the series history, there still don't seem to be much in the way of an audience. Perhaps the most remarkable thing about the series is that it got a chance to prove that it was capable of the faith those few had in it. After the next season, it would be incredibly clear that the faith was justified.