Here's another in my series of explaining the most complicated genre shows or films!
Millions, if not billions, of years ago, meterorites (possibly from Mars) crashed onto Earth, bringing an intelligent alien lifeforce with it. The lifeforce existed in the form of a virus called Purity. Its arrival sparked the beginnings of life on Earth. Alien DNA influenced the evolution of terrestrial lifeforms. The virus eventually infected primitive ancestors of humans and transformed them into grey alien beings known as the Colonists. Many of the Colonists abandoned Earth and went off to colonise the galaxy. They encountered a race of green blooded shapeshifters. The Colonists were able to infect many of the shapeshifters with Purity. It did not alter the shapeshifters into colonists, but did put them under the Colonists' control. They went on to infect and control all other forms of life in the galaxy.
Eventually some of them returned to Earth. In their absence, those left behind had died out in the Ice Age, and humans had successfully evolved into a more sophisticated species, taking over the planet. The virus on Earth had gone dormant, hiding underground in oil deposits. The Colonists began to investigate humans, abducting them. They wiped out the Anasazi Indians, who were sold out by their own leaders who hid inside rock formations with abundant sources of magnetite, a mineral whose presence was lethal to the Colonists. It is possible that the Anasazi had an innate immunity to the virus, making them a threat.
In 1947, a UFO visiting Earth was affected by high levels of magnetite in Roswell, New Mexico, and crashed. The Americans studied the crashed vessel, and met with other great powers in secret UN meetings. An international conspiracy was formed to keep the information quiet, to avoid mass panic. Each country created its own conspiracy organisation, responsible for killing any alien found in its territory, and for studying the aliens and the virus. An arms race began mixed with the Cold War, to see who could weaponise the virus into a biological weapon.
US attempts to mix alien and human DNA failed. Import of scientists captured from the Nazis did not improve matters. By the 1970s, the US conspiracy (the Syndicate) had become autonomous, exerting great influence at a national and international level. They realised that while alien UFO technology could be combatted, the alien virus could not. They therefore made contact with the Colonists and offered a deal. They would pave the way for alien invasion, and in return the Syndicate and their families would be left in a privileged position of an alien dominated Earth. Presumably the Colonists did not have the resources to launch an invasion, so they agreed.
The Colonists demanded that each Syndicate member give up a family member as a hostage. CGB Spender, known as the CIgarette Smoking Man, gave up his wife Cassandra. Bill Mulder, who had helped use the Smallpox vaccination programme to create a giant database of human DNA for the cloning projects, picked his daughter. But he refused to actually hand her over. The Colonists therefore abducted Samantha Mulder directly from her home. Fox Mulder later regained the memories of watching her abduction, fuelling his obsession with the paranormal. Whether or not Bill realised one if not both his children were in fact the product of an affair between his wife and Spender is unknown.
As part of the deal, the Colonists gave the Syndicate a frozen, preserved alien shapeshifter embryo, infected with the virus. Combined with Bill Mulder's database, the Syndicate now had pure sources of human and alien DNA. They began experimenting to create a race of alien/human hybrids. These hybrid clones would initially serve to infiltrate key parts of the country, and would paralyse them at the moment of invasion. Their hybrid nature made them immune to infection by the virus. Bees and other delivery methods were engineered to release the virus to cause mass infection at the right time. In this way, the virus would be spread all over the world at key positions, ensuring there would be no time for anyone to react before it was too late. Syndicate members would receive gene therapy to transform themselves into hybrids, ensuring they would gain immunity to Purity.
Bill Mulder opposed these plans, and forced the Syndicate to agree to an additional backup plan. In secret, they studied the hybrids and the virus, to create a vaccine. If the world population could be immunised against Purity, the alien threat would be minimised. The Russians and others were also rushing ahead with vaccination research. The Colonists themselves planned to betray the Syndicate, wanting to not merely infect humans but in fact wipe them out and replace them with freshly gestated Colonists.
In the mid 90s, FBI Special Agent Fox Mulder had discovered the X Files, a section of files full of cases that could not be solved without an understanding of the paranormal. He began to immerse himself in studying them. His superiors worried at his obsession, and Spender, whose job it was to patrol government agencies like the FBI to ensure they did not interfere with the Syndicate, was concerned. Agent Dana Scully was therefore assigned to debunk Mulder's work. Her scientific and medical background were supposed to aid her in showing Mulder's investigative methods were flawed. In fact, the two worked together remarkably well, solving many difficult cases. They also began to stumble upon more and more findings of Syndicate activities. Eventually they got too close. A key member of the Syndicate, Deep Throat, had become ambivalent in his support of the conspiracy, and had given Mulder too much information. He was therefore murdered, and the X Files shut down. When Mulder persisted in X Files related cases, and a reassigned Scully continued to aid and abet him, the Syndicate moved to stop them. They staged an alien abduction and had Scully removed. She was brutally experimented upon and then dumped. She nonetheless recovered. Their superior, Assistant Director Skinner, stood up to the conspiracy forces by reassigning Mulder and Scully to the X Files.
Mulder and Scully began to piece together parts of the puzzle. Along the way, Scully's sister and Mulder's father were murdered by Syndicate agent Alex Krycek. Krycek in fact was a double agent, infiltrating the US Syndicate for the Russian conspiracy. Mulder discovered his father's role in the conspiracy and that he chose Samantha for abduction. The agents discovered Scully had been exposed to the virus and had her ovaries removed, to provide human DNA for hybrid cloning. Scully discovered her hybrid child, Emily, and was able to take her from the Syndicate, only to watch her die as her body broke down as a failed experiment. She also discovered that the experiments had given her cancer. An implant which monitored Scully's body kept the cancer under control, until removed. Many other abductee women who had also removed their implants were found - all of them died from cancer. Mulder was able to find a replacement chip which again suppressed Scully's cancer. Spender, the smoking man, attempted to bribe Mulder into joining the Syndicate, but failed, and then fell out temporarily with the rest of the Syndicate before rejoining them. Mulder encountered hybrid clones of his sister on several occasions, often being tricked into thinking they were the genuine Samantha Mulder.
Events began to come to a head. Krycek was forced to defect from the Russians and rejoined the Syndicate, bringing with him something the Russians made which the Syndicate had failed at - a vaccine for Purity. It was imperfect, effective only at early stages of infection, but it was a start. Rebel shapeshifters, who had escaped infection, began arriving on Earth. They began attacking abductees, attempting to destroy the Syndicate's attempts to create hybrid clones. They made an offer to the Syndicate of an alliance, which the Syndicate fearfully turned down, concerned at a Colonist reprisal.
The Syndicate again briefly shut the X Files down, and then had it put under the control of Spender's son, ensuring their activities would no longer be investigated by the FBI. Mulder and Scully made allies with Gibson Praise, a young boy whose alien derived genes inherited through evolution were in fact turned on, giving him psychic abilities. They also made contact with Spender's wife Cassandra, a repeat abductee and most promising subject of the cloning project. Eventually the Syndicate succeeded in transforming Cassandra into a hybrid. The Syndicate moved forward to contact the Colonists and trigger the invasion, but were outmaneuvered by shapeshifting Rebels. The rebels infiltrated the Syndicate and wiped them out. The smoking man, Kryeck and two others were the only major members to survive. Spender was outraged that his son had betrayed him and joined Mulder's side, and had him taken away as a test subject.
Mulder at one point was subjected to Russian vaccine tests and exposed to the virus. Radiation from an alien artifact reactivated the dormant virus, and began to activate alien genes. Mulder was crippled by psychic abilities to the extent that his brain began to break down. Scully attempted to investigate the artifact, which was actually an alien craft buried in the sands of Africa, and covered with human genome data, scientific equations, and scriptures from different world religions. Unable to comprehend the mix of science and faith, she returned home to find Spender had abducted Mulder. Spender removed parts of Mulder's transformed tissue and grafted it onto himself, to enable Spender to become a true hybrid. Scully was able to find Mulder and save him. She didn't know that Mulder was still in fact dying from a deteriorative brain condition.
Spender's operation failed - the tissue graft began to kill him. He attempted to capture a crashed UFO to rebuilt the Syndicate but was betrayed by Krycek, who had sold out to the aliens. Shapeshifters were sent to abduct any human whose genome was closely related to the aliens' - such as Mulder. All such humans were abducted one by one, and other forms of evidence related to alien activites was removed. Scully was able to save Gibson Praise from being killed by a shapeshifter, and sent him into hiding, but failed to find Mulder. Agents John Doggett and later Monica Reyes were assigned to aid Scully's work on the X files, in particular in finding Mulder.
Abductees were later found dumped at different points on Earth, in near death states. A rebel alien (or possibly a mere hybrid) named Jeremiah Smith worked to heal them to hinder alien plans, but was himself later removed by the aliens. Mulder's body was found at one site, and later buried. Later it was exhumed and found to be still barely alive. Fortunately Scully realised in time that giving the body warmth and care in fact accelerated the progression of infection of the Purity virus they carried. When Krycek betrayed them again and did not hand over the Russian vaccine, Scully resorted to more mundane methods of antiviral agents and blood transfusions. Eventually through much time and effort she was able to clear Mulder's body of the virus. Another abductee, Billy Miles, was not so lucky. Previously, infection with Purity was shown to either put the host in a coma, or possess them. In some cases, the virus could grow a new Colonist, which burst out of the host body. In these cases, abductees who had active alien DNA were modified by the aliens to transform into something new - a supersoldier. Supersoldiers look entirely human except for a bump on their neck. They are immensely strong. Even if decapitated or entirely shredded into pieces, their bodies can eventually rebuild themselves.
The agents realised that the aliens had abandoned the failed Syndicate and had resorted to replacing humans at key positions with Supersoldiers in the government, FBI and the military. They were also experimenting with human ova, and treating water supplies with chemicals to accelerate human mutation to make them more susceptible to transformation into supersoldiers.
Billy Miles was later sent to wipe out remnant Syndicate operations. They were still trying to make hybrids who could fight the aliens and their virus. The hybrids were mostly gross failures, but one worked perfectly, and was implanted in Scully. The aliens discovered this, and panicked. They initially believed the child to be a perfect melding of human and alien conceived in a barren woman, a perfect entity who was proof of God's existence. They moved to kill Scully, but then changed their minds. They now believed the child would in fact ensure their dominance of the Earth, and allowed Scully to raise the child on their behalf, while they moved forward with their plans. An alien cult attempted to abduct the child, to raise him as a messiah, but were stopped when baby William's unearthly powers activated the alien craft they had uncovered, which wiped the cult out.
Spender's son returned, mutilated by experiments his father had subjected him to. He treated baby Willliam with magnetite, rendering the child a mere mortal. Scully then put William Scully up for anonymous adoption, to give him a normal life and ensure the aliens did not attempt to reverse the process.
Mulder meanwhile had left the FBI. He found the main military base housing the new Supersoldier led conspiracy, and discovered nothing had changed. Nine years of fighting the future had not changed the invasion date of 2012. He was caught and put on trial and sentenced to death by a kangaroo court. His allies helped him escape, and Mulder and Scully went on the run, vowing to fight the aliens.
As the years passed, Scully went to work in a hospital, and Mulder stayed with her in hiding. The aliens abandoned their pursuit, deciding neither of them were a real threat at this point, and continuing with their work.
