The Development of the Black Oil Through Season 4

"Apocrypha" builds upon observations of the Black Oil made in Piper Maru: that an alien life form uses the oil as a medium to "body jump," as Mulder says, using humans as hosts. The oil, "50-weight deisel oil," has also been altered by radiation, raising the question of whether the oil is altered and then serves as a medium, or is altered due to the presence of the alien organism. The first appearance of "decontamination" of the Black Oil occurs in "Apocrypha," in which, the Black Oil being reuinited with its ship, leaves Krycek as he vomits it out every orifice in his face. "Apocrypha," interestingly, also corroborates the flahsback of "Piper Maru," albeit through a flashback within a flashback, whose current point of transmission is unclear. At this point, the flahsback becomes generally accessible, referenced twice in two different episodes. It is true that the title of the episode casts doubt on its validity; apocryphal texts are scriptures whose authenticity or relevance become ultimately unreliable.
The Black Oil, which had previously been limited to context within the last 50 years expands to a larger historical context in season 4. Samples from the rock in the mysterious diplomatic pouch indicate the the material arrived as a part of a 4 billion year old rock which crashed to earth as a part of a meteor in Tunguska, Russia in 1908. Mulder describes this as the greatest cosmic event in the history of civilization, and, in fact, the show's account corresponds with an actual unexplained event. However, the season 4 Black Oil is strikingly different from the Season 3 Black Oil, and questions could be raised at this point in the series as to whether they are actually the same material or organism. In "Tunguska" the Black Oil comes from core samples and the inside of an ancient rock, and assumes a worm-like shape, crawling in order to inhabit its host. Rather than control its host, as seen in Season 3, the wormy oil seems merely to incapacitate. When the geologist examining the rock becomes infected, despite wearing a level 4 HazMat suit, Scully can't at first tell if he's "dead or alive." The inside of his suit is covered with an oily film, and he appears to be in a coma. When Scully and Pendrell later examine the man, Scully finds a "black vermiform organism attached to the pineal gland."(The pineal gland, according to Wikipedia is an " endocrine gland in the vertebrate brain. It produces melatonin, a hormone that affects the modulation of wake/sleep patterns and photoperiodic (seasonal) functions.")It becomes clear in these episodes that the wormy oil is being used in a testing capacity by both Americans and Russians (on the elderly and convicts, respectively), though Vasily Peskov does a fair job at eliminating those responsible and victims of American testing. In the gulag in Tunguska, Mulder becomes part of the experiment as well. The tests are also linked to small pox vaccinations, as they are only performed on those who have been vaccinated and genetically tagged as a result.