The alien life form Purity (or Black Oil, or Black Cancer, or Grey aliens, or the Colonists) created life on Earth and the human race. Its main force left, but it will return to colonize the Earth through a mass viral pandemic, exterminating mankind in the process. The date for the colonization is December 22, 2012. In 1973, a group of people contacted the Colonists and made a deal. In exchange of the survival of this group and their families when the colonization happens, this group would have to prepare the way for this day. This group, which became a global conspiracy, the Syndicate, would have to be turned into alien/human hybrids in order to survive. The Syndicate's task became to create an alien/human hybrid through gene therapy, and to find an effective way to spread the Black Oil virus the day of the colonization. For the hybridization project, civilians were abducted and experimented on in concordance with the aliens. For the spreading, it was decided that it would be done using bees carrying the alien virus, given to them by genetically modified corn. The Syndicate used the military and any other governmental agency, doctors, ex-Axis powers experts, train boxcars, governmental or private buildings and created a clones and hybrids work force, and cataloguing and surveillance systems and facilities.

But like the aliens hid the fact that the human race would be nearly exterminated in the colonization, the Syndicate secretly conducted research for a vaccine that would render one immune to the Black Oil, saving every human being on the planet. There is also a second alien race, the Shapeshifters, who fight against Purity's supremacy. When the search for a vaccine began to give back results, the first successful alien/human hybrid was also created, meaning that the colonization was to begin. But the Syndicate fell victim to the shapeshifting Rebels. After the end of the Syndicate, the infrastructure for the colonization fell to the hands of the colonists. The alien Rebels and the remaining human resistance don't seem enough to prevent the inevitable impending colonization.

The Syndicate's role was filled in by the Supersoldiers, alien facsimilies with human appearance. FBI agents' Mulder and Scully's union resulted in a son, William, who proved to be the subject of a prophecy: to become the leader of the colonization (for this, Mulder must die), or to become the leader of the resistance that will bring colonization down. Scully gave up William for adoption to hide him and Mulder and Scully became fugitives to escape the all-encompassing Supersoldier conspiracy.

Combine that compelling however un-believable storyline with mysterious scripts, atmospheric cinematography and a moody soundscape, and you begin to understand the quality of the X-Files series.