Seasons 7 – 9 (1999–2002)
In November 1999, "The Sixth Extinction" and its second part "Amor Fati" continued the story arc begun in the previous year. New sixth season director Michael Watkins oversaw the latter episode, which was a writing collaboration between Chris Carter and David Duchovny, harkening back to the themes and characters of previous X-Files history — "Anasazi/The Blessing Way/Paper Clip" and Carter's "Redux" trilogy — as well as to The Last Temptation of Christ. However, it was the lowest rated season premiere since 1994's "Little Green Men". Subsequent offerings like "Millennium" (a crossover with Carter's recently canceled other series), and Vince Gilligan's "Hungry" (a sardonic "monster of the week" in which Mulder and Scully barely appeared) and "X-Cops" (an experimental merging with FOX's reality show COPS), did not substantially improve viewership. "Millennium", however, as well as featuring Lance Henriksen reprising his role of Frank Black for the final time, also made waves for showing the first consensual mouth-to-mouth kiss of Mulder and Scully. The occasion was New Year's 2000.
Nick Chinlund also reprised his role of Donnie Pfaster in "Orison", a sequel to season two's "Irresistible", while Ricky Jay played a magician in "The Amazing Maleeni", which contrasted with the generally more emotional tone of season seven. Novelists Tom Maddox and William Gibson returned with a second episode, "First Person Shooter", this time directed by Chris Carter. There were reports of friction between cast and crew, however. David Duchovny, who had filed a lawsuit with FOX that also alleged Carter was paid "hush money" to approve an unfair syndication contract, was reputed to be bored with The X-Files a year after relocating. The show's production costs since the move from Vancouver — typically over $3 million per episode — were also a matter of concern to the network, as it both financed and distributed the show and could not pass off costs to itself without hurting the corporate bottom line.
Breaking the formula of standard stand-alone episodes were several efforts written and directed by the show's stars. Gillian Anderson directed her own script for the metaphysical "all things", further exploring Scully's character. It was the first X-Files to be directed by a woman though the show had had several female writers for periods during seasons 2, 3 and 4 (Carter himself had been subject to a harassment lawsuit years earlier, which was dismissed). Duchovny followed up his prior episode "The Unnatural" with the over-the-top satire, "Hollywood A.D." The title referenced both the Church scandal uncovered therein, and the prospect of Mitch Pileggi's Assistant Director Skinner as a Hollywood player; the self-reflexive episode concerned Skinner's effort to get a blockbuster film made about Mulder and Scully's X-Files investigations, but the "stars" playing the agents are actress Téa Leoni, Duchovny's real life wife as Scully, and comedian Garry Shandling as Mulder. Finally, William Davis, known for his ongoing role as the Cigarette Smoking Man, wrote an episode examining his character, called "En Ami". It was one of Davis' final appearances in the show.
"En Ami" was also director Rob Bowman's final episode for the show. Before the seventh season finale, longtime writer Vince Gilligan also got the chance to direct his first episode, "Je Souhaite" (about a reluctant genie), and Chris Carter turned in the dark slapstick "Fight Club", a return to Carter's roots in comedy. The episode, guest starring Kathy Griffin, did not go over well, particularly so close to what fans expected would be final revelations to the mythology; it holds the record for all time lowest voted episode of the whole series in a survey of viewers.
The final three seasons were a time of closure for The X-Files. Characters within the show were written out, including the Cigarette Smoking Man and Mulder's mother, and several plot threads were resolved, including the fate of Fox Mulder's sister Samantha, who had been a long running plot device within the show, in the episodes "Sein Und Zeit" and "Closure". After settling his contract dispute, David Duchovny quit full-time participation in the show after the seventh season. This contributed to uncertainties over the likelihood of an eighth season. Carter and most fans felt the show was at its natural endpoint with Duchovny's departure, but it was decided Mulder would be abducted at the end of the seventh season, leaving things open for the actor's return in 11 episodes the following year. Season finale "Requiem" was written by Chris Carter as a possible series finale, but the show was again renewed by FOX, despite lower ratings.
For the next two years, Carter was offered incentives to continue the show, which he did despite reservations, concluding there were "more stories to tell." Executive producer and screenwriter Frank Spotnitz was largely responsible, with Carter, for running the show in its final two years, introducing new central characters. With Duchovny's involvement reduced (and in anticipation of Anderson's possible absence in the future), the show's eighth season introduced two new X-Files agents, John Doggett and Monica Reyes (played by Robert Patrick and Annabeth Gish, respectively). Doggett was initially the primary character with Anderson, playing off her in a now-reversed dynamic from The X-Files' earliest seasons, with Scully the "believer" and Doggett the "skeptic", once again investigating paranormal monsters of the week. Carter, Spotnitz, John Shiban and Vince Gilligan continued to serve as writers, with Kim Manners frequently directing, but otherwise the behind the scenes staff experienced turnover.
It was Chris Carter's belief that the series could continue for another ten years with new leads, and the opening credits were accordingly redesigned for the first time in season 9 to emphasize the new actors (along with Pileggi, who was finally listed). This was not to be the case, however, as over the course of the final two seasons, Doggett and Reyes did not provide the ratings boost the producers had hoped for. Following the launch and U.S. commercial failure of spinoff show The Lone Gunmen, whose March 2001 debut episode had dealt with an airplane being hijacked and flown into the World Trade Center, writers were also finding it hard to deal with stock X-Files themes in the wake of the September 11 attacks.
The show received meager Emmy attention in its final years, nevertheless picking up a nomination for Bill Roe's cinematography in "This is Not Happening", and a win for makeup in the stand-alone "Deadalive". Robert Patrick won a Saturn Award for Best Actor, however, and the mythology continued to develop, with a new "super soldiers" concept, and the informer Knowle Rohrer, who interacted with Doggett. Cary Elwes also played a new character. Jeff Gulka's Gibson Praise and Chris Owens' Jeffrey Spender eventually made a return, as well as Scully's mother Margaret, played by Sheila Larken (who had not appeared since the show moved from Vancouver in season 5). The show also alluded to religious allegory in a story line about Scully's pregnancy. It was a seeming reversal of earlier seasons' mythology, in which experiments that had given the character her cancer had also left Scully infertile.
Duchovny returned over the eighth season for several dramatic episodes, and flashbacks were seen in the ninth. Duchovny also directed an episode. Anderson was nominated for her final Screen Actors Guild award as Dana Scully in 2001. The Mulder/Scully relationship by this point reflected what some "shippers" had imagined for years, although others were dissatisfied or offended by the characterizations. The two were eventually joined by Baby William, Scully's child via an implant related to her abduction, while the crew also offered a tribute to an Internet fan fiction writer who had died from cancer in 2001, creating the character of young FBI Agent Leyla Harrison (a self-professed admirer of Mulder and Scully) to honor her memory in the season 8 episode "Alone" and Season 9 episode "Scary Monsters."
The X-Files completed its ninth and final season with the two-hour episode "The Truth", which reunited David Duchovny, Gillian Anderson, and much of the original cast. It first aired on May 19, 2002, finishing third in its timeslot (13.2 million viewers) in the Nielsen ratings, with a slightly lower audience share than the original X-Files pilot episode. The show ceased production at the end of the ninth season — on a cliffhanger, though Carter knew that this would be the final episode. Carter's Ten Thirteen Productions also went into hibernation, and actors, writers, producers and technical staff all moved on to other projects. The show's final Emmy nomination in 2002 went to composer Mark Snow.
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