Sister Act
First off, in Season 7’s "Closure," Mulder accepted the following convoluted version of his sister's disappearance: Samantha was abducted by aliens (in cooperation with the U.S. Government) and subjected to multiple abductions during which she endured many horrible tests. For six years, between kidnappings, she lived in California as the sister of Jeffery Spender and the daughter of the Cigarette Smoking Man. When she was 14, she ran away and before she could be recaptured, she was rescued by mystical beings called "walk-ins," who transformed her into pure energy before she could be harmed. Some didn’t find this answer as satisfying as Mulder did, but as far as Chris Carter and Co. were concerned, the Samantha chapter appeared to be closed.The Life and Death and Infection of Fox Mulder
Mulder was abducted by aliens at the end of the seventh season and became the subject of the same terrible treatments his sister had faced. With Mulder gone, Scully was left to tackle the X-Files with John Doggett (Robert Patrick), a skeptic tough-guy whose only son had been murdered years before. A lot of storylines in these later seasons revolved around the "super soldiers" - almost indestructible alien-human hybrids designed by the government to replace humans when the aliens invade… we think?Mulder was ultimately infected with an alien virus and returned as a corpse. His body was buried, but he wasn't exactly dead - the virus allowed him to remain alive even as he was decomposing… because he was in the process of becoming an alien-hybrid, but was saved through surgery and antibiotics and…Look, it's better not to dwell on it, trust me. A resurrected Mulder started investigating X-Files again, even though Assistant Director Kersh told him not to. Kersh, played by Grey's Anatomy's James Pickens, Jr., was one of several villains the show used to replace the frankly irreplaceable Cigarette Smoking Man, who was still believed to be dead during this time. Kersh eventually got ticked off enough to fire Mulder from the Bureau. Of cours, Fox couldn't stop himself from trying to find out the truth about the aliens, the military, and how a once-barren Scully could get pregnant.Throughout her pregnancy, Scully fought against the constant suggestion that her baby's origins were supernatural. In the Season 8 finale, "Existence," everyone's favorite one-armed, two-faced assassin, Alex Krycek, tried to prevent the child from being born. Failing that, he then tried to kill Mulder and was shot through the head by Skinner.Season 9 picked up with Mulder having gone into hiding. It was subsequently revealed that Mulder was laying low in New Mexico with the help of chess-prodigy and mind-reader, Gibson Praise.
Doggett and Reyes and Scully, Oh My!
Scully, meanwhile, was ostensibly off the X-Files and back to teaching forensic pathology at the FBI Academy in Quantico. Of course, she found herself drawn into several cases by her former partner John Doggett, who was now investigating the supernatural with the spiritual and open-minded Monica Reyes (Annabeth Gish).Mulder's absence left Scully to raise her (possibly their) son, William, on her own. This was no picnic, as people were constantly trying to drug, abduct and kill the poor kid, who began to frighten his mother by causing his crib mobile to turn without touching it and making alien artifacts spin around his head for fun. William was hinted at being one of several things: 1) a part-alien hybrid born as a result of Scully's abduction years earlier 2) a super-human baby created by divine intervention to eventually defeat the alien invaders, 3) a human baby conceived through in-vitro fertilization, with Mulder as the sperm donor, or 4) a baby conceived through off-camera (though undoubtedly hot) sex between Mulder and Scully.
[In the 2008 X-Files feature film, I Want to Believe, when Scully feels a connection to a sick boy who is about William’s age, Mulder does refer to him as “our son,” seemingly confirming he is the father.]
In these later days of the series, the Lone Gunmen were killed off. After their short-lived spinoff ended, Frohike, Langly and Byers sealed themselves in an airtight chamber with a terrorist in order to prevent him from unleashing a horrific virus upon humanity. They were, improbably, buried at Arlington National Cemetery. Continue to Page 2, as we delve into the very last days of the original series and the second X-Files movie.
Brother, Can You Spare a Spender?
Throughout this time, Dana pined for Fox and the pair exchanged loving emails. Later, she feared that Mulder might be dead (again) or at least in mortal danger. She encountered a horrendously disfigured man who sought her help, and she briefly feared that this poor soul was what was left of Mulder. His DNA even turned out to be very similar to Mulder's (in the episode, it's said to be “a match”), but later he's revealed to be Jeffery Spender, Mulder's half-brother - probably because Mulder's mom had an affair with Spender's dad, the Cigarette Smoking Man, but possibly because Mulder's father slept around with Spender's mother, Cassandra. Again, Chris Carter wasn't really into giving us definitive answers.After Spender injected his nephew with some kind of iron-rich substance to "save" him, Scully determined he would always be a target, so she made the painful decision to put him up for adoption. He was ultimately sent to Wyoming to be raised lovingly and anonymously by new parents, and where he is now, presumably, a happy and healthy teenager who occasionally moves objects with his mind.The End (For Now)
When Mulder finally turned up in the series finale "The Truth," he was captured after breaking into a top-secret government installation, but not before learning the date that aliens would supposedly come and take over the planet: December 22, 2012. [I’m sure some had heard of that whole end of the Mayan calendar thing before the X-Files finale, but remember how it actually became a rather mainstream concern?]Mulder "killed" super soldier/alien replacement/what-the-heck-ever Knowle Rohrer (played by Adam Baldwin) and was put on trial for murder. He talked to several ghosts during the episode (Krycek, The Lone Gunmen, Mr. X) though it's unclear whether he's imagining these characters as part of his conscience, if something supernatural or spiritual was occurring or if he'd finally gone crazy. Mulder was given a "This Is Your Life" type trial, where various former recurring characters try to save him by recapping the show's convoluted mythology, while Skinner acted, oddly, as Mulder's lawyer. Among Mulder's supporters were Spender, Scully and icy-blond informant Marita Covarrubias (The Walking Dead's Laurie Holden).Since all of these witnesses of course sounded crazy talking about aliens infiltrating the government and cloning and abductions and whatnot, plus the fact that the kangaroo court was presided over by Alan Dale's "Toothpick Man" (an alien conspirator and another pseudo-stand-in for The Cigarette Smoking Man), Mulder was convicted but promptly broken out of prison by Skinner and sudden good-guy Assistant Director Kersh. Mulder and Scully determined to go into hiding, and then journeyed to a New Mexican pueblo because Fox wanted to get answers from the actually-still-alive Cigarette Smoking Man, who merely used the opportunity to taunt Mulder about having wasted his life, which Mulder seemed to take to heart.
A not-dead Knowle Rohrer showed up to kill Mulder and Scully, but Doggett and Reyes arrived and saved them. As they fled, an unmarked helicopter fired a missile into Cancer Man's pueblo, and he's seemingly obliterated. In the show's final scene, Scully and Mulder bunkered down in a Roswell motel room. Mulder was depressed over the futility of his quest for the truth, and his inability to stop the coming alien invasion he fears is inevitable. Scully tried to convince him that they could still fight the future and was able to lift his spirits, leaving Mulder hopeful that there may be a higher power at work in the universe, and maybe they aren't doomed after all. They cuddled on the bed, seemingly devoted to one another.
Still Wanting to Believe After All These Years...
The last time the characters appeared on-screen, in the aforementioned movie I Want to Believe, Scully was working as an oncologist in a Catholic hospital and living with Mulder, who was in hiding and still conspiracy-obsessed. In order to help find a missing FBI agent however, Mulder was pardoned, because he’s the only one who can talk to self-described psychics (just go with it). Working on the case reinvigorated Mulder, but put a strain on his romantic relationship with Scully, who wanted to put all the darkness and monster-hunting behind them. At the end of the film -- which centered on a non-mythology case – the two were still together as a couple……Though we know the return of the series will begin with them reunited after some time apart. What happened in-between and what’s next for Mulder and Scully? Hopefully the truth awaits us when The X-Files returns on Sunday, January 24th.
Christine Seghers is a writer at IGN TV. She lives in her own little world and rarely interacts with people, but you can still attempt to follow her on Twitter at @CMSeghers and IGN at ChristineSeghers.