Season 6 (1998–1999)
Over the course of the previous two years, the show had built upon the mythology storylines that grew in complexity and prominence (and confusion, especially for new viewers) as the show progressed. The loyalties of the Cigarette Smoking Man and Krycek were continually shifting and the influence of CSM appeared to be waning. Above all, the Syndicate's co-operation with the colonizers was proven to be a ploy, as they were secretly attempting to develop a vaccine to the black oil (also known as "purity") which was shown to be an agent which would allow for the transportation of alien beings, and which would be spread through bees come the time for colonization. However, another alien faction was proven to exist, and these rebels opposed the colonists and the Syndicate for their co-operation. Consequently, in mid-season 6 "full disclosure" episodes "Two Fathers" and "One Son", the rebels destroyed the Syndicate.
At the end of The X-Files film, the X-Files had again been re-opened. However, Agents Spender and Fowley were assigned to them rather than Mulder and Scully, who were reassigned from Walter Skinner — who continued to appear on the show, nevertheless — to a new boss, Assistant Director Alvin Kersh (played by James Pickens, Jr.). Gibson Praise was dispatched in the first episode of season 6, "The Beginning" (which also posited a possible alien source for humanity), and Jeffrey Spender was also written out of the show during season 6, while Mimi Rogers' Diana Fowley continued to play a role and appeared quite close to the Cigarette Smoking Man. The latter character was finally given a name, CGB Spender, and an identity — father of Jeffrey and ex-husband of Cassandra.
With the move to Los Angeles, California in season 6, many changes behind the scenes occurred, as much of the original X-Files crew was gone. New production designer Corey Kaplan, editor Lynne Willingham, writer David Amann, and director and producer Michael Watkins would stay on for several years. Bill Roe became the show's new director of photography, and episodes generally had a drier, brighter look due to the sunshine and climate of California, as compared with the rain, fog and temperate forests of Vancouver, Canada. Early in the sixth season, the producers took advantage of the new location, setting the show in parts of the country they had not been able to write episodes in previously. For example, Vince Gilligan's "Drive" (about a man subject to an unexplained illness) was a frenetic action episode, unusual for The X-Files, not least due to its setting on roads in the stark desert of Nevada. The "Dreamland" two-parter was also set in Nevada, this time in the legendary Area 51. It marked another comedy outing for the show, in a season increasingly light in tone, with guest star Michael McKean playing man in black Morris Fletcher, who switches bodies with Fox Mulder during the course of the episodes. It is the only non-mythology two part episode of The X-Files.
The sixth season also explored the ever-deepening bond between Mulder and Scully. The episode "Triangle" was Chris Carter's fifth try at directing as well as writing The X-Files. With its ambitious mise-en-scène featuring continuous takes and split screens, and its setting on an ocean liner on the eve of World War II (played by RMS Queen Mary anchored in Long Beach, California), it was widely seen as a bid for an Emmy Award, which Carter did not receive, though the episode was up for sound editing. "Triangle" concerned Mulder's trip to the Bermuda Triangle to investigate an X-File there, disobeying superiors such as Kersh, in parallel with Scully and The Lone Gunmen's dogged efforts to locate him, contrasting this with time warp versions of all the main characters in September 1939, and ending with a pivotal "shipper" moment while leaving both the preceding events and the agents' relationship ambiguous. Whether they "should" or "should not" consummate their "platonic" love was a matter of immense debate among the fan community for years, and is still subject to scrutiny, since even after abundant hints Carter refuses to substantiate whether the two characters ever had sex. Other episodes that season, such as "The Rain King", "Monday", "Field Trip", and Carter's "Milagro" and "How the Ghosts Stole Christmas" (guest starring Ed Asner and Lily Tomlin), also dealt primarily with romantic relationships and alternate realities, using these to comment on Mulder and Scully's status.
Late in the season, David Duchovny — who had a master's degree in English and considered a career as a writer before joining the cast— contributed his first solo X-Files script, "The Unnatural", which he also directed. It was about Josh "Ex" Exley, a baseball-loving alien who played in the Negro Leagues after the fabled Roswell crash in 1947. A baseball announcer in "The Unnatural" was voiced by famous Los Angeles Dodgers announcer Vin Scully, Chris Carter's original inspiration for the name of Dana Scully. The episode was also originally set to feature the involvement of Darren McGavin, star of early X-Files inspiration Kolchak: The Night Stalker. McGavin had to pull out due to illness, but he does appear as original X-File investigator Agent Arthur Dales in season five's "Travelers" and season six's "Agua Mala" (about Mulder and Scully's discovery of a dangerous water-based life form during a hurricane in Florida).
Some longtime fans were alienated by the show in season 6, due to the different tone taken by most stand-alone episodes after the move to Los Angeles. Rather than adhering to the previous style of "monsters of the week", they were often romantic or gently humorous or both, such as "Arcadia", where Mulder and Scully pose as a married couple in a gated community in order to solve a case, or the darker, campy "Terms of Endearment", starring Bruce Campbell as a demon. Meanwhile, some felt there was no coherent plan to the mytharc, that Carter was "making it all up as he goes along".The show ended season 6 with solid ratings, but its lowest average since season two, beginning a decline that would continue for the final three years of its run. This may have been due to different competition on Sunday nights, or because viewers felt the show was burning out or even "jumping the shark" (the show would actually reference the concept in its episode "Jump the Shark" three years later). The show's producers acknowledged they had been trying to do something different from previous years in season six. The X-Files was nevertheless FOX's highest rated show that year, and was nominated for eight Emmys in 1999, winning one for makeup. It was also nominated for SAG Awards for Anderson, Duchovny and Outstanding Performance by an Ensemble Cast, recognizing Pileggi, Pickens, Owens and Davis' continuing contributions.
As compared with other seasons, relatively few mythology episodes were made during season 6, only "The Beginning", the stand-alone "S.R. 819" (in which Walter Skinner's health is compromised by a mysterious nanotechnology affliction as possible blackmail to force him to turn against Mulder and Scully), "Two Fathers" and "One Son", and the season finale "Biogenesis", the first of a three-part story continued into season 7, about Scully's investigation of an ancient UFO discovered off the coast of West Africa and effects on Mulder from it.
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