The storylines were widely affected by the pregnancy of actress Gillian Anderson; it was decided that Scully would be kidnapped and abducted by aliens, explaining her absence and allowing her to appear comatose two episodes later, which ultimately added more intricacies to the mythology.

Dana Scully (Gillian Anderson) is reassigned to teach at the FBI Academy while Fox Mulder (David Duchovny) is given lowly surveillance assignments.

After he investigates extraterrestrial cases at the Arecibo Observatory in Puerto Rico,[1][2] Mulder is given a new partner, Alex Krycek (Nicholas Lea), and meets a secretive informant, X (Steven Williams).

[5][6] Barry eventually kidnaps Scully, believing that if he brings her to his original abduction site, Skyland Mountain, aliens will take her instead of him.

[9][10] The agents later investigate a case involving alien biology being injected into teenagers in Wisconsin, and once again they encounter Deep Throat's killer, who is killed by the local sheriff.

[19] Instead, co-executive producers Glen Morgan, James Wong and Howard Gordon penned the opening premiere, "Little Green Men"; the episode was the first entry to actually show an alien in the series.

[19] As the series ended its first season, a problem had arisen for the producers: the pregnancy of Gillian Anderson, who played Dana Scully.

[21] Though they considered having Scully giving birth to an alien child, the producers decided to work around Anderson's pregnancy by having her abducted and appearing comatose several episodes later.

[22] This was described by executive producer Frank Spotnitz as "the best thing that ever happened to the series" as it helped form the intricate mythology that would run throughout the show.

[22] To hide Anderson's pregnancy in the early episodes, the producers disguised it with "very fancy trick angles, trench coats, and scenes where she is seated rather than standing".

[24] The two-parter of Carter's "Duane Barry" and Paul Brown's "Ascension" were scripted to culminate in Scully's abduction and the re-opening of the X-Files.

X was originally intended to be a woman with Natalija Nogulich already cast in the role, but was replaced by Williams as the writers did not believe she had the "right chemistry" with her co-stars.

[27] Nicholas Lea, who had previously appeared in a small part in the season one's "Gender Bender", was cast as Alex Krycek.

"[30] Carter was positive towards the idea and acted upon it, creating with Spotnitz the character of the Alien Bounty Hunter for the two-part episodes "Colony" and "End Game".

[31] Darren McGavin, star of Kolchak: The Night Stalker, was sought out for the part of Senator Matheson in "Little Green Men" and Mulder's father in "Colony" and "End Game", but the roles went to Raymond J. Barry and Peter Donat respectively, while McGavin agreed to play X-Files founder Arthur Dales in season five.

[33] Series creator Chris Carter directed one episode, making his directorial debut,[34] while Daniel Sackheim, Michael Lange, James Contner, James Whitmore, Jr., Michael Vejar, Nick Marck, Stephen Surjik and Win Phelps each directed one episode.

[60] The season hit a low with the twenty-first episode, "The Calusari", which was viewed by 7.9 million households and received a rating of 8.3/16.

The review highlighted "The Host", "Duane Barry" and "Ascension", the cliffhanger finale "Anasazi", the "unforgettable" "Humbug", and meeting Mulder and Scully's families in "Colony" and "One Breath".

[63] IGN gave the season a rating of 9 out of 10, with the reviewer noting it was an improvement upon the first as it had "started to explore a little" and the "evolution of the characters makes the product shine even though the plotlines have begun to seem familiar".

[64] Robert Shearman and Lars Pearson, in their book Wanting to Believe: A Critical Guide to The X-Files, Millennium & The Lone Gunmen, rated several episodes across the season highly, awarding five stars out of five to "Little Green Men", "Duane Barry", "One Breath", "Irresistible", "Die Hand Die Verletzt", and "Anasazi".