14 years after The X-Files Season 9, there are less concise explanations or summaries of The X-Files Alien Mythology Arc (mytharc) than I thought there would be. For those who seek to understand what happened before the new 2016 series, here’s my take, edited from sources from various wikipedia.
Obviously, this whole article is a huge spoiler.
Mulder & Scully
The protagonist in the X-Files series, Fox Mulder, is obsessed with the unexplained / paranormal X-Files cases of FBI, because his sister Samantha was abducted by aliens. He is joined by Dana Scully, originally sent to debunk his work. Together they uncovered a government conspiracy:
The original inhabitant of this planet is alien. Having arrived here millions of years ago, they walked the planet long before the dinosaurs did. Most of them left during the last ice age because their viral form is deactivated by extreme cold. Those that did not leave have been lying dormant, underground in the form of an evolved viral pathogen known as Black Oil / Purity / Black Cancer. This virus has been waiting to be reconstituted by the alien race when it comes to colonize the planet, using human bodies as hosts.
One of the alien ships crashed in Roswell in 1947 due to the presence of magnetite in the surrounding rocks. From this accident governments learned of the alien Colonists’ plans. A shadow government known as the Syndicate was formed, and they threatened the aliens to destroy the planet with nuclear weapons, thereby resulting in the planet becoming uninhabitable to the alien Colonists due to extreme cold. As such, humanity was spared immediate invasion, and the Syndicate began negotiations with them.
An agreement was reached that both sides began to work on creating an alien-human hybrid, which would serve as a slave race for the Colonists. In exchange for the Colonists’ cooperation, the Syndicate handed over their family members, in return they got alien embryos as a source of genetic material for the hybrid experiments. Fox Mulder’s legal father, Bill Mulder, reluctantly gave up Samantha for this purpose, and hoped that she would survive the takeover as a genetic hybrid. The Syndicate oversaw plans to aid the colonization by preparing to have bees spreading the virus from genetically altered pollen in corn.
Secretly, the Syndicate attempted to develop a vaccine for the black oil virus in an effort to save all of humanity. What they did not know originally, however, was that the black oil virus did not just control the human body, but could also mutate to give birth to new aliens, resulting in the repopulation of aliens instead of colonization.
Downfall of the Syndicate
Eventually the Syndicate successfully created the first alien-human hybrid, implying that colonization could begin immediately. Before they could inform the Colonists, most of the Syndicate and the hybrid were killed by Alien Rebels. The rebels are the same species of the Colonists, but they are not infected by the black oil, and oppose the colonization.
Then super-soldiers appeared. They look human but are actually aliens. They were created to protect the alien repopulation. With the Syndicate mostly dead, the super-soldiers were in control of key government positions. At the end of Season 9, it was finally revealed that the date of of colonization was December 22, 2012 – the end of Mayan calendar.
So what about Samantha? Throughout Fox Mulder’s investigation, he met a lot of clones of Samantha. The real Samantha, however, turned out to have been returned by the aliens a long time ago. She was then taken to an air force base to continue to be experimented on. She escaped, but just before she was going to be recaptured by the Syndicate, she was taken by “spiritual intervention” beings called “Walk-ins”, which try to save the innocent souls of children who are doomed to suffer terrible fates. So she was dead, and her soul was in a better place.
In the 2016 mini-series, it is retconned that alien invasion did not happen, and the conspiracy above is just a hoax, in order to cover up people using alien technology to take over the world. (The real reason that alien invasion did not happen, is probably because the third movie was not greenlit.)