It’s time to dive into the crazy chaos of The X-Files’ mythology once again. As I already mentioned in the season summary: Nearly every single mythology episode of this season tells its own story and they seem to be totally unconnected. So I’m pretty sure this is going to be a lot of fun to sort it all out. Maybe. Or is there a hidden red threat we overlooked all the time? Let’s find out!
What we know from season 1: Aliens abduct people, experiment on them, sometimes kill them after the experiments fail. There was a hidden metal implant found in some abductees necks.
We get some descriptions from Duane Barry about being abducted and tested on by a group of aliens [2×05]. Although he may be a pathological lier his story is plausible and proven by several metal implants found in his body. One implants shows a bar code that scanned by an ordinary checkout scanner triggers some strange behaviour of the machine. Even though this scene is close to ridiculous it implies the abductors may not all be so alien after all.
This case seems to be even less alien-related. Although Scully gets taken away in a mysterious light on top of a mountain [2×06] everything else looks nothing like the work of aliens. Obviously the Cigarette Smoking Man is in control of taking Scully and bringing her back [2×08]. Her blood shows signs of experiments with alien DNA the government did on several other occasions. And finally her name (and Barry’s) appear on a top-secret government document about extra-terrestrial activity. But if the government is behind all of this – why send a man to steal her blood after she was returned to the hospital? No implications of her abduction are known yet, so it’s pretty hard to guess any reason behind it.
What we know from season 1: Thev’ve been here for a long time and sometimes they crash their ships. There are multi-national procedures established to kill surviving aliens since they are deadly armed and can turn invisible.
May be hard to tell crash from deliberate landing as at least one UFO going down in the sea is totally fine [2×15] and also able to disable subs with high-pitched frequency signals [2×16]. We see an alien as a long thin shape [2×01] and several more aliens as small figures with big heads, although this might be heavily biased since these scenes are from the memory of mentally-ill Duany Barry (and it’s actually unclear whether he was abducted by aliens at all) [2×05]. We also learn that aliens can only (?) be killed by piercing the base of the neck with an ice pick shaped weapon [2×15] dissolving them into green blood which is toxic for humans similar to what we saw on test persons of Purity Control. There is an alien bounty hunter on Earth hunting down alien renegaders who tried to build up their own society. At least the bounty hunter has the ability to shape-shift and perfectly impersonate any human being.
Military UFO technology
What we know from season 1: The military is in possession of UFOs and uses some of the alien technology.
We get nothing new about alien technology in the hands of the military this season.
Experiments on alien DNA
What we know from season 1: Project “Purity Control” is using an alien virus for treatment of terminally ill human beings.
We encounter Project “Purity Control” another time this season when a small town population is used unwillingly as test subjects. People infected with the alien substance via eating infected meat begin to behave strange and feel like possessed by spirits [2×10]. The test case is terminated and covered up. The alien virus used for “Purity Control” is part of the alien blood [2×17] and can be deactivated with low temperature. This also explains why the enhanced humans’ blood from season one behaves as toxic as the aliens’ blood. The government seems to have done tests on real alien test subjects as we see a lot of alien bodies with smallpox vaccination marks buried in the desert [2×25].
What we know from season 1: All alien-related events are covered up by people in or above the FBI, the Cigarette Smoking Guy being one of them. They are suspicious of and interfering with Mulder’s work. Mulder’s informant Deep Throat is killed at the end of the season.
Young FBI agent Alex Krycek is introduced as the Cigarette Smoking Man’s henchman [2×05]. He hinders Mulder from saving Scully from abduction and presumably kills Duane Barry in order to cover up the case [2×06]. This is a strong indication of the conspiracy being behind Scully’s abduction instead of aliens. Krycek also kills Mulder’s father [2×25]. Although deliberately not doing this in the past the CSM finally tries to kill Mulder by giving order to destroy the box car he’s in. Bill Mulder worked together with the CSM in the past and had something to do with the top-secret government file about extraterrestrial life Mulder gets hand on. There is a multi-national Syndicate guarding the file (and the secrets behind it) which the CSM is part of. It’s heavily implied by Scully’s name inside the file that the Syndicate (and thereby Bill Mulder) has something to do with Scully’s abduction and that there’s a link between this event and the alien DNA experiments. Mulder gets a new informant inside the FBI called X [2×02]. Other then Deep Throat although helping Mulder on some occasions [2×04/15/17] X often tries to stop Mulder from pursuing his goals [2×07] or even betrays him [2×23].
What we know from season 1: Not much. She was abducted when she was twelve years old.
We get to see Samantha’s abduction showing her floating into a white light. Although this version might be biased being the memory of young Fox Mulder it strongly indicates her being abducted by aliens. Later Samantha returns home [2×16] but is identified as an alone clone [2×17]. Whether or not it’s a clone of real Samantha or just some random woman is not totally clear. The bounty hunter reveals real Samantha still being alive.
Unrelated Alien Stories
There is a crude story about pregnant zoo animals being taken away and return invisible and not pregnant anymore [2×18]. It’s presumed this is part of an alien conservation program.
Unrelated Conspiracy Stories
Two episodes center around government conspiracies without connecting them to the main arc. A whole town is part of an experiment which contaminates people with an LSD-like substance and influences their actions by manipulating electronic devices in order to show orders on their displays [2×03]. The men behind the experiment are aware of Mulder investigating and even hack into his phone in the end. Also there’s an incident when some prisoner’s infected with a contagious disease escape from prison. The infection is linked to experiments of a major pharmaceutical corporation and greatly covered up by government and CDC [2×22].