Two things have a bad habit of showing up on your typical X-files episode:
(Hey, this isn't bad when you consider how many times time travel
shows up in the Star Trek franchise)
"Tunguska", was an example of the latter (though the former may show up in the conclusion for all we know). At the end of it, Mulder was in some Russian gulag, strapped down to a table. Moments later, the black goo, containing the 'oil slick' aliens (first seen in last season's "Piper Maru"), were dumped on him, which quickly infested his body. Just before the momentous fade-out, it was apparent that Mulder had been 'possessed' by the oil slick aliens. So how is he going to get out of this one?
One possibility is that the bandaged wound on his arm (which looks suspiciously like a smallpox vaccination) was some kind of a protective agent against the oil slick aliens. The purpose of the gulag may have been to test some kind of defense against these alien's. The other possibility is that Mulder will survive the oil slick possession the same way Krycek did, when they were attracted to something else of interest. However, in most cases, it seemed that when the parasites jumped from host to host, the former host died. Somehow Krycek was able to avoid the same fate. Whatever the outcome, what I'm more interested in is how the Krycek plot thread will be developed and how these oil slick aliens fit into the whole scheme of things.
One more note: was Mulder being uncharacteristically evil in this episode? First, after leaving the home of the mysterious SGSC woman, he hits Krycek after getting back into the car. It was an act of malice that seemed totally out of character for Mulder (like the time when he punched Skinner in "Anasazi" when he was under the influence). Sure Krycek killed Mulder's father, but I thought Mulder would have a better sense of honour than that, lowering himself to Smoking Man and his thugs (but then again, he did pull a gun on CSM when Scully was abducted). The other strange scene was when Mulder parked the car at the airport. He was going to leave Krycek handcuffed to the car for who-knows-how-long... until Mulder found out that he could speak Russian. He really looked as though he was going to do it. This type of behaviour is unbecoming of a soldier of truth like Mulder... it's almost as blasphemous as seeing Scully smoking!
So what was revealed in part two of "Tunguska"?
So what do these revelations mean to the conspiracy mythology of the X-Files?
CSM has said before that he believes that he is doing the right thing, and that exposure of the secrets he keeps would cause great upheaval in society. Could it be that the shadow government is actually trying to prevent the spread of this black cancer, which may be the prelude to an alien invasion? Or is the shadow government merely trying to develop the black cancer as an offensive weapon, and utilizing their research on civilians as a means to test the effectiveness of its method of prophylaxis?
If it is the former, then this would change the entire dynamic of the relationships between the various stakeholders of the X-files. What Mulder and Scully may have stumbled onto is a conspiracy designed to protect the country from an insidious subversion by the shapechanging aliens... who may be utilizing the black cancer to achieve their ends. If that is the case, then Mulder is becoming the unwitting pawn of the shapechangers.
Note that the smallpox vaccinations were carried out on the civilian population, the prisoners in the gulag, and the dead aliens in the boxcar in the New Mexico desert. Both the shadow government and the shapechanging aliens have smallpox vaccination records on file (in a West Virginia mine and the computer files of the various Jebediah Smiths, respectively). Each smallpox vaccination has a distinct nucleopeptide sequence which serves as a market to identify each individual. Could it be that the shadow government created the smallpox vaccine as a means of innoculating the world's population against the threat of alien-bourne disease (the black cancer), leading the way to colonization? And are the Jebediah Smiths are using the same records to find susceptible individuals who were not innoculated (since they were all working in social services offices across the country, they had access to the entire current database of American citizens). This adversarial role of the aliens would also explain the U.N. Security Council's General Resolution No. 1013, stating that any government that recovers a live alien is responsible for its immediate disposal.
So in this interpretation, the attempts to develop an alien-human hybrid by the shadow government may be to bulk up the gene pool by introducing the aliens' supposed resistance to the black cancer. The woman at SGSC is not Mulder's friend, but is actually manipulating him to set back the efforts of the shadow government. Hell, the same could be said for Deep Throat and Mr. X. Note that everytime Mulder and Scully get too close to the work of the shadow government, all traces of the work become erased, no doubt setting back the research, either by stopping it or slowing it down.
Or is this black cancer merely a cloak-and-dagger type of game? In the second season "Colony" episode, it was a Russian pilot that crash landed in the Beaufort Sea who was rescued. Eventually, the Russian pilot made it to an abortion clinic in Scranton, where it killed a doctor. Eventually, this Russian pilot, the alien bounty hunter, kills other doctors, who are all clones, around the country. Mulder is initially told that all the doctors being killed are Soviet 'spy clones' who are being killed under a secret agreement. Perhaps everything we've seen in the X-files is part of a disinformation campaign to cover-up these espionage activities-- is the shadow government trying to protect itself from Russian interference? Are the shapechangers actually Russian agents?