The X-Files

"Sleepless" introduced Agent Alex Krycek (Nicholas Lea) as Mulder's new partner. Their partnership would last only into the next two episodes, "Duane Barry" and "Ascension," which proved crucial to the fate of the series. Searching for a solution to the now acute problem of Anderson's pregnancy, Carter and his writers decided to have her abducted by Duane Barry (Steve Railsback), himself a likely alien abductee, in the episode, "Duane Barry." The episode was both written and directed by Carter (his debut) and received several Emmy nominations the following year.[52]

Anderson did not appear at all in the episode "3", but mysteriously returned in Morgan and Wong's "One Breath" (directed by R. W. Goodwin), an episode which consistently scores among the highest in fan ratings.[53] Scully's abduction provoked an existential crisis in Mulder. Although the show left it up in the air for years as to who was directly responsible (aliens, the government, or some combination of both), the earlier episode "Sleepless" had foreshadowed the events with the Cigarette Smoking Man's declaration that "every problem has a solution" (referring to Scully). Scully was now seen to be firmly on Mulder's side in the larger conflict, regardless of her original role as a debunker and her continued skepticism towards the paranormal.

After Scully's recovery (and the birth of Anderson's daughter, Piper), Mulder and Scully returned to work on the re-opened X-Files, investigating cases ranging from Haitian zombies ("Fresh Bones") to animal abductions ("Fearful Symmetry") and exorcism ("The Calusari"). This period would see the show gain more mainstream appeal, often earning winning scores during its Friday night timeslot.[54] Its Nielsen ratings rose to their highest peaks thus-far with the occult-themed "Die Hand Die Verletzt" and the epic "Colony"/"End Game".[4] The latter was a two-part episode introducing the idea of colonization, the Alien Bounty Hunter, as well as the characters Bill (Peter Donat) and Teena (Rebecca Toolan) Mulder, Fox Mulder's parents.
"Die Hand Die Verletzt" was Morgan and Wong's final X-Files script until the fourth season, as they departed to start their own series Space: Above and Beyond, but at the same time there was new involvement behind the scenes. The episode also marked the X-Files directorial debut of Kim Manners, who would stay with the show until its end and direct the largest number of episodes of the series. On "Colony", star David Duchovny collaborated with Chris Carter on the story, the first of Duchovny's involvements in writing for the show. Frank Spotnitz, a new story editor brought on by Chris Carter, wrote "End Game", the second of the two-part episode; Spotnitz would be a producer and writer on The X-Files and other Ten Thirteen projects for years and had a key role in shaping the mythology. The middle of the second season also saw "Irresistible", an episode directed by David Nutter and written by Chris Carter, which Carter later credited as a blueprint for his even darker show Millennium.[34] This was the first non-paranormal episode of The X-Files, dealing with the trauma of investigating Donnie Pfaster, a "death fetishist" (so named instead of "necrophiliac" to get past the FOX censors).[55] A sequel, "Orison", was made in the seventh season.

During its second season, The X Files finished 64th out of 141 shows, a marked improvement from the first season. The ratings were not spectacular, but the series had attracted enough fans to be classified as a "cult hit," particularly by Fox standards. Most importantly it made great gains among the 18-to-49 age demographic sought by advertisers.[54][32] The show was chosen as Best Television Show of 1994 by Entertainment Weekly and named best drama by the Television Critics Association, and it received seven Emmy nominations, mostly in the technical categories, with one nomination for best drama series.[39] In 1995, The X-Files won a Golden Globe Award for best television drama, winning out over several more established series such as ER, Picket Fences and NYPD Blue.[56]

The last weeks of season two brought more changes, beginning what some saw as The X-Files' peak creative period.[57] The Edgar Award-nominated "Humbug," an unconventional standalone episode about a small town inhabited by circus sideshow performers, was the first script fully written by Darin Morgan. At the time it was also considered a risky experiment, as it was the first outright comedy episode. Gillian Anderson famously swallowed a real cricket in one ad-libbed scene.[58] Eventual senior writer Vince Gilligan also offered his first episode, the darker sci-fi "Soft Light", guest starring Tony Shalhoub as a remorseful physicist whose shadow kills people.

Season two ended in May 1995 with "Anasazi" (co-written by Carter with David Duchovny), which attracted widespread attention with its cliffhanger ending[54] and put the future of the mythology up in the air. In the episode, Mulder and Scully are contacted by a computer hacker who has gained access to the Majestic-12 documents. Now-free agent Alex Krycek also made his first reappearance since "Ascension". The episode began a three-part arc, the show's most ambitious mythology episodes thus-far, which extended into the third season and centering around Navajo former code talker, Albert Hosteen (Floyd Red Crow Westerman).[59] The show could not afford location filming, so a rock quarry in British Columbia was painted to match the desert hues of the American Southwest.[13] Outside the U.S., The X-Files was by now one of the most popular shows in the world,[57] and was being broadcast in 60 countries.