No one crafted a mystery better than The X-Files. Well, for the first few seasons, at least. By the end of the series initial run, things had kind of gone off the rails. The more recent episodes were solid but failed to capture the same magic fans had been given years earlier.
But even with those additional episodes, there were still a few mysteries that were left unsolved and a few questions left unanswered, particularly in regards to the main characters. But that's not surprising for a show that thrived on never giving fans the complete truth.
Skinner's Wife
FBI Assistant Director Walter Skinner had a rough go of it during The X-Files. As one of the people whose job it was to supervise Fox Mulder, he probably spent a lot of time in the double facepalm position at his desk. He'd probably have an easier time as the principal of Springfield Elementary.
But at least he has family to go home to. Maybe. Skinner's wife, Sharon, was not mentioned frequently though she was around. They were married for a long time, possibly separated and reconciled, and she eventually died. All of that is really unclear, though, and her true fate, as well as Skinner's marital status, remain a bit confusing.
Poisoned By Black Oil
The coming alien invasion and the Earth-based Syndicate that seems to be trying to help the coming storm along had a lot of tricks up their collective sleeves. One of them was the Black Oil, a substance referred to by the Russians who have encountered it as the Black Cancer.
It's real name was Purity, and was a virus made from the life force of the alien colonists that was capable of taking control of other beings. Fox Mulder was exposed to the Black Oil at one point, though he never started exhibiting any of the symptoms or issues associated with the exposure, something that has yet to be explained.
The Spartan Virus
Fox's exposure to the Spartan Virus was a much different situation. When The-X-Files came back for new episodes, the Spartan Virus was at the center of the Cigarette Smoking Man's nefarious plan to wipe out the vast majority of human life by attacking their immune systems.
Aliens, and alien-human hybrids, were immune to it. This included Dana Scully as she had alien DNA in her system thanks to her previous alien abductions. The weird thing was that Mulder was not immune, despite also being exposed to alien DNA. That being said, it's hard to compare him to Scully as she might be immortal.
Scully Might Be Immortal
A running gag through several episodes of the series was the idea that Scully might be immortal. It all started in season three when a man who could foresee people's deaths told Scully she would never die. It comes up again in season six when an immortal photographer takes Scully's place when death comes for her, possibly making her immortal.
Beyond that, incidents keep coming up in the series that seem to support the theory. But it could also just be the show's writers messing with fans after reading their fiction. Still, it's an idea with some merit that has never been resolved.
Mulder's Boxcar Escape
Chasing aliens lands you in some very stranger predicaments. Take Mulder ending up inside a buried boxcar filled with the corpses of alien-human hybrids. That doesn't really happen to most people. It's a long series of very specific life choices that lead you to moments like that. Once trapped in the boxcar, the Cigarette Smoking Man firebombed it, presumably leaving Mulder to die.
In the first episode of the next season, Mulder was lying outside the boxcar, half-buried in rocks. The person who found him talked about also finding bodies of alien-human hybrids on the ground there after they escaped through a tunnel. Presumably, Fox did the same thing, though that's never explicitly stated. He also might just be immortal like Scully.
John Doggett's Fate
When David Duchovny left The X-Files close to the end of its original run, he took the character of Fox Mulder with him. But the paranormal waits for no man so someone else stepped in to help Scully, FBI Special Agent John Doggett. Robert Patrick played the character throughout season nine, even acting in Mulder's defense in the final episode.
But since then, Doggett has been MIA. When Scully left, she was replaced by Monica Reyes, who got some form of closure in the new episodes. Doggett has not, suddenly becoming absent from the story despite the importance he played in it.
The Death Of The Cigarette Smoking Man
It's hard to imagine The X-Files without the Cigarette Smoking Man. He was originally meant to be nothing more than an extra lurking around in the background of Skinner's office in the pilot. Fans responded so well to him that he grew to be the show's main antagonist. While more details were eventually revealed about CSM, the character was better when he was mysterious and far more menacing.
The finale of the most recent season brought some finality to the character as Mulder shot and killed him. But the Cigarette Smoking Man has died before. Without more episodes, fans will never know for sure if that was his swan song.
Scully's Visions
For someone who still struggles to believe in the supernatural, Scully sure has a lot of unexplained visions that help her solve cases. It's not like they happen in every episode but they happen enough that they are a thing that should be investigated more fully.
The strange part is people don't seem to be as concerned about them as they should be. Some minor explanations have been given but that doesn't change the fact that Scully has a surprising number of conveniently timed visions.
Samantha Clones
The driving force behind Mulder's obsession has always been the abduction of his sister Samantha by aliens at a young age. His search for the truth behind her disappearance has informed almost every life choice he has made, for better or worse.
Eventually, he finds out the insane details behind the abduction and that she passed away years ago. But a whole pile of clones of her still exist. The aliens used her DNA to make multiple series of Samantha clones for a variety of purposes, sometimes just to screw with Mulder. The one question that has never been answered is if there are more clones still out there.
Skinner's Sacrifice
The finale of the most recent season featured the X-Files team taking on the Cigarette Smoking Man in an effort to stop him. They appeared to succeed, but at a cost. Skinner may have sacrificed himself for the greater good and got hit by a car. The injuries he sustained could have been life-threatening but were also survivable.
Since there was no season to follow it up, no one really knows if Skinner is alive and well. Some fans like to believe that he's happily enjoying a steamed ham with Superintendent Chalmers. Wait, that's the wrong Skinner. Still, some closure on the character would be marvelous.