With their discovery by modern humankind, the aliens had to revise their plans for invasion or risk the united efforts of Earth to repel them. Unfortunately, the greed of government and military leaders for survival and power made this all to easy.
First contact led not only to the awareness of the aliens existence but also direct communication with the aliens themselves by government officials, first from the US and then all countries. The aliens were soon able to convince all those officials with the inevitable eventuality of their success. Faced with this reality, these government officials opted to cooperate with the aliens to prepare the earth for colonization in hopes of saving themselves. The aliens thus began working with a certain groups of humans who operated as a shadow government (for the Western allies this was known as The Syndicate) who would help prepare earth for a mass invasion and colonization.
The Work of the Syndicate: Mass infection
For the Syndicate, their part of the bargain was twofold. Firstly, they would assist in creating a means to spread the black oil infection which they believed would turn humanity into slaves. In return, they were promised for themselves and their families not to be infected. (Unfortunately for the Mulder family and others, they had to turn over a family member as collateral on this promise.) This also included the location, mining, and transportation of the black virus from deposits around the world under the guise of oil refining missions. There were experiments with spreading the infection through money, inhalers, and a host of other mechanisms, but the most successful was apparently genetically altered crops and the bees that pollinate them.
The Work of the Syndicate: Alien-Human Hybrids
The second task of the Syndicate was to arrange for experimentation towards the creation of a set of alien-human hybrids which would be immune to the black oil. The Syndicate was given alien DNA in order to work on such a hybrid in an ironically named program called “Purity”. In the meantime, the aliens were given access to key government positions in Social Security and medical research facilities so as to conduct research for the project and track appropriate. Clones (different from a true hybrid) were supposedly also created and worked in these positions as well. (Though these may simply have been morphed aliens given a false identity so the Syndicate would not be suspicious of their presence.) The experiments at this time included alien abductions, government cataloguing, the use of information about human experimentation by Nazi/Japanese scientists in World War II, and many “mistakes” which were discarded (the majority of alien bodies seen by Mulder). The Syndicate thus assisted the aliens in not only in the process of abducting individuals identified for experimentation but also using government resources to cover up all problems or alien sightings and spread disinformation.
The Secret Agenda of the Syndicate
Despite their seeming temerity in the face of the alien threat, many members of the Syndicate (like Bill Mulder) were actually cooperating to buy time as they sought to find a way to fight against the colonization plans. This including using the DNA provided to work on a secret sub-project to develop a vaccine for the black oil infection which was labelled as “Purity Control”. Tests were conducted in military bases and on unwitting nursing home patients in the US and on gulag prisoners in Russia. They eventually succeeded in the late 1990’s.
The Secret Agenda of the Aliens
Though they were able to convince the Syndicate of their superiority, one can assume that the aliens’ desire to work with these individuals in secretly spreading the black oil was to avoid allowing mankind to fight back—showing that the aliens are not all-powerful. Unknown to the Syndicate, however, the distribution of the black oil to hosts throughout the world would not result in an enslaved human population. Instead, the virus was actually a life-stage of the aliens themselves, one which would eventually gestate and allow the large-scale re-population of the aliens and the total destruction of human kind. The creation of a alien-human hybrid would be the catalyst for this event.