The X-Files' first feature film, Fight The Future, was a turning point in the series for a number of reasons, not least of which being the final introduction of total, unambiguous aliens into the plot. (That they turned out to be something more akin to the body horror xenomorphs of Alien than the little green men from abduction stories I'm not complaining about). This, of course, is something that had been hinted at extensively, but never conclusively documented, and always with a considerable amount of room for skeptical doubt built into every apparent revelation regarding the possibility of other intelligent life in the universe making contact with Earth.
But in spite of being essentially one big tease, this actually worked out pretty well, for a number of reasons. To start with, it ensured that The X-Files would be taken (by its creators as much as its audience) as a serious and intelligent exploration into the realm of extreme possibility, instead of an outright science-fiction extravaganza, with different alien races popping up every week (I'm not going to mention any names - Star Trek). But the writers also mined that uncertainty of knowing whether the alien conspiracy was true or not for some great drama up through the series' fifth season.
"I promise you Mulder won’t see a spaceship on this show for five years."
- Chris Carter pitching the show, as reported in a TV Guide interview from May 1998
I must have heard this quote paraphrased indirectly, because I always thought he had referred to aliens specifically, and not spaceships (although it's a great irony that Mulder sees a spaceship - albeit a military one - in just the second episode). I don't think the difference is very important, though. The same conclusion can be drawn either way, and I think aliens are more fun to talk about. (Spaceship aficionados will surely want to check out the episodes Deep Throat, Fallen Angel, Paper Clip, Jose Chung's 'From Outer Space', Tempus Fugit, and The Red and the Black).
I'd like to take some time to discuss all the aliens that appeared in the series prior to the season six premiere, which followed the movie. Yes, there were aliens (unless there weren't), but you never saw them clearly. They were always hiding off-screen, or when you did see them, they took either human or non-substantial form (no doubt taking a lot of pressure off of the special effects department, especially in those early years), or could be written off as the potential hallucination of a delusional psychotic, or the deformed result of some kind of gruesome medical experiment on humans. Let's explore.
Spoiler Warning: It should go without saying - but in case it doesn't - that the rest of this post will contain spoilers from throughout the series' first five seasons.
Nearly No-Shows
Several episodes in the series deal with alien abductions, but without giving the audience so much as a peek at any actual aliens. All we see are bright lights, and the after-effects of the aliens' interference in people's lives. This is true of the pilot episode, as well as Conduit, and Fearful Symmetry (which deals with animal abductions).
In other cases, we get brief or distorted views of what we are expected to believe are aliens, such as the tall doorway silhouette in Little Green Men that shows up twice - first, in Mulder's dream of his sister's abduction, and then again, during a close encounter.
There is also a group of short, elfin figures that brush past Scully in a darkened tunnel in the episode Paper Clip, on their way to (apparently) boarding a UFO. Their connection to similar creatures witnessed in the preceding episode, The Blessing Way, is inconclusive, as evidence suggests that the latter may not in fact be truly alien (see below).
What could be considered to be a real and true alien pilot appears in the episode Fallen Angel, after its craft crash lands on Earth. But the alien is disguised by some kind of camouflage - an invisible cloaking device (like the Predators use) - so that we can't actually see it.
On the subject of aliens we don't see, there is also an alleged alien pilot being transported across the country in the episode E.B.E., but we never do get to see it - just the empty, child-sized stretcher it was allegedly carried on.
Hybrids, Hunters, Clones, and Drones
Human-alien hybrids (first encountered in The Erlenmeyer Flask, and later explored in Emily) are distinguished mainly by their green blood, which is toxic to humans. Otherwise they appear perfectly human. They exhibit different skills in different episodes, including superhuman strength, the ability to breathe underwater, shape-shifting, and miraculous powers of healing (as demonstrated in Talitha Cumi).
The Alien Bounty Hunter (introduced in Colony) - even if he is a full alien - may be considered to be a variation on this theme, as he never appears in the form of anything other than human, and has many of the same attributes.
Some of the hybrids occur in groups of clones (including Mulder's sister Samantha, seen in End Game), and sometimes as drones (which Mulder discovers in Herrenvolk) - which are stunted clones in the form of children with limited functioning, much like worker bees. Other clones are spotted in the episode Memento Mori.
A variation of the Alien Bounty Hunter appears in Patient X/The Red and the Black. These faceless rebels have engaged in self-mutilation in order to avoid contamination by the Black Oil.
Black Oil
The Black Oil is not humanoid, but does not look like a traditional alien, either. It is - as its description suggests - simply a sentient, black oil. However, it has the habit of infecting human hosts, enabling "alien" characters to again be played by human actors (with a little digital black film swimming over their eyes).
In Piper Maru/Apocrypha, the Black Oil is able to control the mind of its host, and pass from one body to another. In Tunguska/Terma, it behaves a little differently. Originating from a Martian meteorite, its infected host goes into a catatonic state. The Black Oil appears again in Patient X/The Red and the Black, exhibiting an inconsistent combination of its previous abilities. Its true significance is not revealed until the movie.
Other Species
Most non-mythology, freak-of-the-week episodes deal with organisms and paranormal entities that are more-or-less terrestrial. There are a couple, however, in the first season, that involve entities originating from outer space.
The episode Ice features a parasitic alien worm discovered in an impact crater buried under Alaskan ice. Although the show's mythology covers alien infections and lifeform-bearing meteorites, they seem to have no connection to this one-off monster-of-the-week.
The very next episode, Space, features a ghost that does not have a corporeal form, but instead chooses to possess a former astronaut haunted by the face on Mars. It has no significant connection to the show's mythology either.
Alleged Aliens
Our first glimpse of anything that looks extraterrestrial is the cryogenically frozen alien fetus in The Erlenmeyer Flask, from which source was extracted the virus used in that episode's experiments with ET gene therapy to produce human-alien hybrids. Deep Throat claims that this tissue (and presumably others like it) were recovered from a number of Roswell-like incidents.
The episode Duane Barry really gives us our first and best look at traditional grey aliens in the process of performing an abduction. We see them crowding around a man's bed at night, and later around a strange operating table while esoteric medical tests are being performed on the unlucky abductee. Occurring early in the second season, this would appear to be a blatant violation of the "no aliens" rule, except that everything we see can be written off as the hallucinations of a psychotic. Either way, it makes for some harrowing programming.
A later episode, El Mundo Gira, features a scene that interprets the Mexican legend of el chupacabra (the goat sucker) as alien visitors - but this is pretty clearly framed as the imaginative exaggeration of a suggestible storyteller.
Even more provocative, Jose Chung's 'From Outer Space' ostensibly features traditional alien abductors, except this time they are revealed to be human Air Force pilots in alien costumes. One wonders if this might not be the case in previous abductions, too - such as those witnessed in Duane Barry. There is another "alien" - Lord Kinbote - but it is more of a Cyclopean monstrosity that comes not from outer space, but inner space (which, technically, makes it not an extraterrestrial). Also, it may not really be there.
In Anasazi, an earthquake uncovers a boxcar filled with corpses that appear to be extraterrestrial. Once again, the evidence here is provocative (even more so than the probably simian corpse unearthed in the pilot), but alternative explanations are provided.
By the end of the three-part myth arc, Mulder is convinced that they were the failed results of secret government testing to create human-alien hybrids. But in Nisei/731, in which similar, living creatures are encountered in what, at first glance, appears to be an alien internment camp, Scully puts forth another hypothesis - that they are merely the severely deformed bodies of humans subjected to disfiguring medical experiments by Axis power scientists given amnesty after the war.
In Musings of a Cigarette Smoking Man, we witness Deep Throat executing what appears to be a full-grown E.B.E., lying inactive on a stretcher. Mostly consistent with the story Deep Throat fed Mulder in the episode E.B.E., it is rather larger than what the stretcher in that episode would have been able to hold. One must consider, however, that the events of this episode may be little more than the egotistical daydreams of a megalomaniac.
Tempus Fugit/Max features a couple of alien abductions, but as previously, we don't ever see the aliens involved - except for the one that dies underwater in a UFO crash. It's dead, so it just lays there, but at least we can see more of it than the invisible form in Fallen Angel.
Finally, we come to Gethsemane, in which Mulder not only discovers an alien corpus frozen in the Canadian wilderness, but has a chance to examine it up close, while a colleague performs a full autopsy on it. This is about as damning as evidence can get, but this also happens to be the episode where Mulder learns that the entire alien conspiracy is a fabrication - an elaborate hoax designed as a smokescreen to deflect attention away from the military's expenditures.
In Redux, Mulder infiltrates a Defense Department storage facility loaded with fake alien bodies, which could explain what was seen in previous episodes such as Tempus Fugit, and The Erlenmeyer Flask. The hoax will itself ultimately turn out to be a lie, but after this level of doubt has been generated, only the direct observation of a living, breathing, unambiguously extraterrestrial biological entity will be enough to convince Mulder (and the audience) that aliens really are involved in the conspiracy somehow.
And that's exactly what Fight The Future - and the sixth season premiere - accomplishes.