Previously: The X-Files Season 1 Mythology Guide
The X-Files have been shut down, Mulder and Scully are working on different assignments, it seems as if the show’s basic premise was short lived. Of course nothing could stop Mulder and nothing could destroy the bond between him and Scully so their quest continues, although it becomes more dangerous. The first episode of the second season sees Mulder go AWOL following a clue from his friend in congress, Senator Matheson, which leads him to a close encounter in Puerto Rico. It’s the start of a journey which sees him uncover a wealth of new information about the alien conspiracy.
Season 2 – What We Learn
Although the first episode of the season is very much alien-centric, offering a glimpse of a visitation as Mulder rushes to obtain proof of their existence, it’s the two-parter, ‘Duane Barry’ and ‘Ascension’, where the main alien myth-arc begins. A storyline concocted to give Gillian Anderson a break following the birth of her first child, Scully’s abduction, and the results of it, form a crucial element of the series going forward. It all starts when multiple abductee Duane Barry trades himself for Scully when he knows he’s going to be taken by aliens again.
Duane Barry is a former FBI agent and his testimony confirms that the government knows about and is involved with the abductions. Flashbacks reveal that the last time he was in abducted was in 1985, and in the present day after being hospitalised by an FBI sniper, evidence of an alien abduction is found in his body. This evidence includes strange metal objects in his abdomen as well as in his sinuses and impossibly tiny holes drilled into his teeth. Prior to being taken Scully tries scanning one of the metal objects through a checkout scanner causing it to go berserk. Telling Mulder her discovery on the phone, she makes the first reference to the chips being used to catalogue people.
Before this, in the episode ‘Sleepless’, we are introduced to a new character, Alex Krycek. In the episode he is revealed to be a plant working for the Cigarette Smoking Man and identifies Scully as a significant threat. It’s implied that Scully’s abduction was part of one of CSM’s elaborate plans. In the final episode of the season he will murder Mulder’s father under orders from CSM.
While Mulder may get a new enemy this season he also gets a new friend, X (or Mr X), an informant who replaces the more avuncular Deep Throat.
Later on we’re introduced to a new part of the alien conspiracy, the Clones. Seemingly bred in the image of alien abductees such as Mulder’s sister. The first type of clone we’re introduced to in the series is the exact copy, a version of Samantha as she would have looked had she not been abducted. The Samantha series of clones were accompanied by a Gregor series, a male type of a previously unseen character. According to Samantha, the clones managed to successfully combine human and alien DNA, the aim of alien hybridisation to eradicate the identical nature of the clones so they can live together. She also claims that because this attempt at colonisation wasn’t done with the consent of the aliens a bounty hunter has been dispatched to dispose of them.
It’s at this point the Alien Bounty Hunter is introduced for the first time, his mission to destroy the clones. The Bounty Hunter is a shapeshifter, able to assume to form of any human being in order to elude capture.
The series comes to a head with the cliff-hanger ‘Anasazi’ where it becomes clear that there has been some kind of exchange going on between the government and the Grey aliens. Thanks to a hacker Mulder get his hands on the government’s complete files of alien activity on Earth. Unfortunately, it’s all encrypted in Navajo, a Native American language that few people can read. However, Native American code reader called Albert Hosteen, though Scully, is able to decipher parts of it including references to herself, Duane Barry and “merchandise”. It’s also revealed that William Mulder once worked with CSM and was involved with the alien conspiracy. Still suffering from the loss of his father and a gunshot wound to the shoulder, Mulder’s search leads for answers him to a box car, buried in the desert, and filled with alien corpses. The alien corpses bear smallpox vaccination scars and it starts to become clear what has been going on.
It’s also in the closing episode of the season that we get our first glimpse a mysterious group which will become better defined in Season 3 (and later known as the Syndicate), although the main members aren’t introduced yet, as CSM is called upon to track down the hacked files by various international officials.