In an attempt to clarify some of this, we are giving the floor this week to Joshua Hall-Bachner, who recently posted the following excellent treatise on the X-Files Conspiracy to the alt.tv.x-files newsgroup. Only time (and Chris Carter) will tell how close this comes to the truth, but it is a fine piece of work in any case. The text which follows is reprinted here with Joshua's kind permission.

Here, I will attempt to explain, as well as possible, how all the various aspects of the conspiracy on The X-Files join together, in the light of the information revealed in the movie. All my comments are annotated with a [source in brackets], when available; if there is no source listed, it means it is only my speculation/deduction and cannot be taken as canonical.

The series will air a 2 parter in the sixth season that will clear up a few of the mis-understandings in the show's murky mythology. It will air in Febuary!

Abbreviations:

FTF: The X-Files Movie (for its slogan, "Fight the Future") CCSM: Chris Carter Soundtrack Message (from the last track of the X-Files Movie Soundtrack.)

It all begins thousands of years ago. The Aliens (referred hereafter as "Greens") whom we've seen so often, in the form of the bounty hunter ["Colony/End Game", "Talitha Cumi"/"Herrenvolk", etc.] and Jeremiah Smith ["Talitha Cumi", "Herrenvolk"] among others, landed and surveyed the planet Earth. [FTF] For some reason, though, the Greens decided to forego colonization of our lovely little planet at the time.

Flash forward to 1948. The Greens decide that they are ready to colonize Earth. Rather than invade themselves, they strike up a deal with various members of the world governments: in exchange for preparing Earth for a painless colonization, they would be allowed to survive beyond the colonization, like "the French Vichy government [played a role in] the German final solution." [CCSM] The group known as "The Syndicate" originally were only in charge of covering up the plan, keeping it hidden from the world. However, as time went on, they slowly wrested power from the others in control, so that by the present day they were not only in complete control of the colonization operation, but were in fact more powerful than any other government organization, taking orders from no one but Syndicate leader Conrad Strughold. [CCSM] The Syndicate has many times used the "UFO myth" -- and its poor standing outside of the fanatical "believer" community -- to hide its activities from the world, by making those who might discover part of their operation look foolish to the world. [CCSM]

The Greens' colonization plan all centers on their most powerful weapon: a genetically engineered virus commonly found in the form of a "black oil." This oil has appeared several times on the show, each in a slightly different form ["Piper Maru", "Tunguska", "The Red and The Black"]; in addition, we've seen it in two new forms in the movie [FTF]. The Tunguska oil is the closest to the form that the Syndicate has been planning for, with none of the odd effects of the Piper Maru oil (radiation) or the movie oil (gestation): it simply controls the victim's mind, making him into a slave of the Greens. The oil is merely a carrier for the important part, though: the virus' DNA payload which actually causes the oil's negative effects.

The Syndicate has two responsibilities to accomplish for the Greens. The first involves spreading the virus. The current form we all know and love, the black oil, is not a terribly efficient method, nor is it particularly easy to use. The Greens want every person in the world infected, after all. Therefore, the Syndicate has hit upon a remarkably subtle method of delivery: Africanized (aka Killer) Bees. By having them pollinate specially-bred plants, genetically crossed with the oil virus, they can deliver the virus to anyone they sting. [FTF] The movie is the first time we've seen bees actually carrying the black oil virus; previously, we've seen the Syndicate's "beta tests" of the bee technology, testing the bees on plants genetically altered with smallpox DNA to make sure they can deliver it correctly before switching to the virus-carrying corn. ["Herrenvolk", "Zero Sum"]

The second half of their syndicate's job is to create an alien-human hybrid. This project, known as "Purity Control" ["The Erlenmeyer Flask", CCSM] is the older of the two, stretching back to the first contact with the Greens. The purpose of this is to create a group of beings, seemingly human at first glance, but loyal to the alien colonists -- and immune to the effects of the black oil. [CCSM, "Christmas Carol/Emily"] In this way, when the aliens arrive, the hybrids will have the world completely prepared for colonization. (As a convenient side effect, these hybrids make the perfect workers to tend the genetically-altered plants carrying the virus, as they are immune to its effects. ["Herrenvolk", "Zero Sum"]) The preparations for this breeding program are far-reaching, touching upon almost every federal agency in the United States. The genetic material for the cloning experiments is taken from "abductees," in the form of gamete cells ["Memento Mori"]. During their abduction, each abductee has a small "chip" inserted into their neck, which, when stimulated by a certain signal, causes them to converge on the nearest "hot spot." ["Patient X", "The Red and The Black"] (The purpose of this is currently unknown.) Removing the chip starts the spread of a strange cancer, fundamentally uncurable, through the abductee's system. ["Nisei", "Memento Mori", "Gethsemane"] (The purpose of this cancer is also currently unknown.)

In addition, the Syndicate has detailed records on every person in the U.S. under 35; a genetic sample is taken from each person during their smallpox inoculation, and a molecular "marker," like those for tracking animals in the wild, inserted into the scar ["Paper Clip"], allowing the Syndicate to keep tabs on every person on the planet, determine their suitability as a genetic donor, and (presumably) catalog them once colonization has begun.

The Greens have stayed fairly hands-off during this entire process, as the entire purpose of the deal with the Syndicate was to allow the aliens to simply colonize the planet, without worry. (****) Their major contribution to the project has been their "bounty hunters," expert alien assassins who can shift their appearance at will. These aliens serve the double purpose of aiding the Syndicate with their project, and making sure the project remains on-course.

Unbeknownst to the Greens, however, the Syndicate has a third objective: develop a vaccine/antidote to the black oil. If they can do so without the Greens' knowledge, they might be able to foil their plans and avert the colonization. [CCSM] Eventually, we learn that the Russians, who are evidently not involved in the Syndicate but who have also been attempting to develop a vaccine, succeeded before the Syndicate, and had been testing their vaccine on live suspects. ["Terma"] Eventually, through a deal with Krycek, the Syndicate managed to acquire the vaccine themselves. However, they have not yet begun the process of using it.

Also making things difficult for the Greens is a small faction of anti-colonization aliens, who have been attempting to stop the colonization effort by destroying one of the neccesary parts of the colonization plans -- the abductees. By sending off the signal to the chips implanted in the abductee's necks, then killing them, the rebels hoped to prevent the colonization from taking place. Of course, this didn't happen quite like they intended...

Recent events have, for perhaps the first time, come as a complete shock to the Syndicate. The discovery of an ancient sample of the black oil, from when the Greens originally walked the Earth, has a very different effect from the one they knew: it uses the body mass of a victim to create a new, ravenously violent alien life form. Despite the evidence that the Greens have been lying to them all along, the Syndicate (mostly) decide to continue on with the project as-is, using the new virus rather than the old one in their genetically altered corn.