Section 1 : Biogenesis
From the Big Bang to the 20th Century
Purity [Black Oil, Black Cancer]
At the beginning was Purity.
It can be encountered in many forms.
Purity is very old, even older than terrestrial life itself. It has been theorized that natural evolution of Purity was progressively bringing it closer to extinction. Then, Purity made up a plan majestic in size and time span. Throughout the Galaxy, it would create life or help its development on different planets and guide the evolution of life through billions of years until a being suitable for gestation would appear. Until then, Purity would be in stasis, waiting. Purity would then take over this being, gestate and effectively create an entirely new population of greys: a colonization, or a blossoming renaissance. On Earth, this host being would be the human race. After billions of years of evolution and space-faring, Purity's force was dried down; by having a planet in which Purity could gather strength again and be reinvigorated would be a safe bet for prolonged survival of the race.
Sources: 1X23: The Erlenmeyer Flask, 3X15: Piper Maru, 4X09: Tunguska, Fight the Future, 6X01: The Beginning, 6X11: Two Fathers, 6X22: Biogenesis, 7X03: The Sixth Extinction, 7X22: Requiem
Shapeshifters and Faceless Rebels
Purity created the race of the Shapeshifters, using its own genome as a blueprint. The Shapeshifters physically resemble humans, they can be infected by Purity, but they can change the shape of their bodies to some degree and heal themselves and others (using the palm of their hands). A green substance flows in their veins, extremely similar to the greys' only that it doesn't carry the Black Oil virus in it, which means the Shapeshifters are not immune to the Black Oil. The race of the Shapeshifters was developed and developed itself on a planet that belongs to the constellation of Cassiopeia. When the time was ripe, Purity colonized the planet of the Shapeshifters, exterminating most of them. Those who survived created a resistance movement, leading a guerilla war against Purity. They mutilated themselves so as not to be infected by Purity, and were called the Faceless Rebels.
A Shapeshifter is a host more resistant than a human. To infiltrate Earth, Purity used Shapeshifter hosts. Purity performed genetic tests on the Shapeshifters; one of these was cloned and his clones were infected by Purity: these Purity-controlled Shapeshifters are the Alien Bounty Hunters. The original non-infected Shapeshifter that was cloned escaped, freeing some of his non-infected clones with him. They joined the Rebels, with the original one as their leader.
Terrestrial Biogenesis and the Colonization project
Some 3.7 billion years ago, Purity arrived on a still barren Earth and created life using much of the primordial soup material already present, but also genetic material of the Black Oil itself. Purity left, though some of it lay dormant underground, in oil deposits or underground caves or outpost ships. For billions of years, the technology Purity left behind orchestrated terrestrial evolution, influencing natural evolution and triggering massive extinctions that made way to new species.
All this led to the premeditated creation of mankind, further using genetic material of Purity and that of terrestrial organisms. Large parts of the alien DNA were embedded in the human DNA and were turned off; these would serve as guidelines for the creation of a full alien organism when the Black Oil virus would infect the host. Humanity's cultural evolution was encouraged by Purity's technology, to which mankind owes the sacred texts of great religions (Judaism, Christianity, Islam); 'miracles' were performed to support these religions, like Moses' plagues, or healings and resurrections.
Humans thrived and filled the Earth, according to Purity's plan. Any humans that became infected by the Black Oil when they would discover an underground deposit were taken to a large craft, buried under the Antarctic ice, that would later be known as Base 1. There, they were put in stasis, slowing down the gestation process of the grey alien until a reawakening when the colonization would come. The date for colonization was set to December 22, 2012 AD.
The Anasazi American Indians adopted Purity's writing and language. Because of the great knowledge the Anasazi attained of Purity, they were abducted and hunted down to be exterminated. Knowledge of Purity's writing still survives today among the Navajo Indians.
Sources: 2X25: Anasazi, Fight the Future, 6X01: The Beginning, 6X22: Biogenesis, 7X03: The Sixth Extinction, Anne Simon's "The Real Science behind the X-Files"
Tunguska and Black Cancer
The same biogenesis effort had been attempted on Mars: Purity had brought life to a planet that at the time seemed promising. But life there did not thrive and Mars eventually became a desert planet; the only living thing that survived there was Black Oil, hidden underground like on Earth.
In 1908, in Siberia, a meteorite fell and devastated the landscape. The meteorite was in fact Martian rock, expelled in space by some random cosmic event. Inside the rock was Black Oil; it was very weakened by the shock of crashing on Earth -- so much so that when it entered a human host, it did not actively take control of it but barely put the host into a coma. This Black Oil was unable to move the body of the host or to trigger a gestation; for this reason, the Russians who found it called Purity "Black Cancer".
The Russians saw the military potential of a virus-like organism that induced coma: it could be used as a very effective biological weapon. Eventually, it came to the hands of Iraqi leader Saddam Hussein, who used it against US troops in the Gulf War (1989-1991). In this way, samples of the Black Cancer came to the hands of the american government.