The X-Files played host to several different variations in its ongoing mythology arc, including one concerning an alien virus dubbed the black oil. As many grotesque monsters, and underhanded government agents that The X-Files showcased over the years, there's no doubt that when most people think of the show, aliens come to mind. After all, proving the existence of extraterrestrial life was Mulder's main quest for most of the show's run, tying back to his - it turns out mistaken - belief that he had witnessed his sister Samantha be abducted when they were children.
Aliens are as much part of the show's visual iconography as anything else, or indeed even Mulder and Scully themselves, most often personified by flying saucers. While Mulder never did succeed in exposing alien life to the world at large, he did at least ultimately convince the notoriously skeptical Scully they were real, which on a personal level, is probably a much bigger achievement. It turns out the truth really was out there, even if it didn't end up becoming public.
While the alien conspiracy - and their human co-conspirators, known as The Syndicate - had many dastardly plans for mankind, most tied back in some way to the black oil. On a show as full of mysteries as The X-Files, it's not surprising that the complete details of how the black oil works and where it came from aren't fully known. However, what we do know about it is still pretty terrifying.
X-Files: The Black Oil Has Ancient Origins
It's theorized that the black oil virus is the sentient life force of the aliens who wish to colonize Earth, with help from the Syndicate. To that end, it's said that the black oil's existence on Earth actually predates humans, but it chose to leave Earth due to the ice age, as while extreme cold doesn't kill the black oil, it does put it in a sort of suspended animation. By 35,000 B.C., as depicted in the opening scenes of 1998 movie The X-Files: Fight the Future, the black oil and the aliens it powers have returned, and after fighting with a pair of cavemen, manages to infect one of them.
By 1945, a squad of P-51 Mustang fighter planes were escorting a B-29 bomber carrying a nuclear weapon, when a UFO appeared. The crafts engaged in hostilities, then crashed into the ocean. Later that year, the U.S. sent a military submarine named the Zeus Faber down to locate the wreckage. They did so, but ended up exposed to the black oil in the process, which infected their captain. Of 144 crew members, only 7 made it back alive, thanks to a power to emit huge blasts of deadly radiation possessed by those taken over by the black oil. This is detailed in season 3's "Piper Maru/Apocrypha" two-part episode.
X-Files: The 1990s Black Oil Emergence
In 1995, the American government sent a salvage team in to recover the UFO from the ocean, but the squadron of planes was left behind. The following year, a French salvage ship called the Piper Maru discovered the planes, but during the operation, a diver named Bernard Gaultier was possessed by the black oil, and was able to safely transport his ship and now radiation sick crew to California. The UFO was being held in San Diego, and Gaultier lived in San Francisco, enabling him to spread the infection to his wife, who then spread it to X-Files antagonist Alex Krycek, who of course betrayed Mulder as always and returned the substance to its ship. Not that he came out well, becoming trapped inside a silo for an extended period.
Later in 1996, a Russian site discovered space rocks containing the black oil in Tunguska, and attempts were made to smuggle the substance into the U.S. to cause further spread. Krycek again reluctantly partners with Mulder and Scully to gain possession of a rock and the black oil within. Mulder and Krycek follow the trail back to Russia, where Krycek unsurprisingly turns on Mulder yet again, leading him to become infected with the black oil. Thankfully, the Russians have developed a working vaccine to its effects. Russia's government is able to cover up the brief U.S. outbreak, as the Syndicate aren't the only ones capable of making their problems disappear. Krycek is later able to bring a sample of the Russian vaccine back to the Syndicate for bargaining purposes.
X-Files: The Seeming Defeat of the Black Oil
In The X-Files: Fight the Future movie, Mulder and Scully discover that part of the Syndicate's plot to facilitate alien colonization of Earth is to unleash genetically engineered bees that will infect humanity with the black oil. Scully gets infected, but is saved by a vaccine given to Mulder by a wavering member of the Syndicate. The black oil then faded into the background until 2001, during season 8's "Vienen", when Mulder and Doggett reluctantly work together to take down an oil rig in the Gulf of Mexico that's tapped into the black oil and seen its crew get infected. Mulder succeeds, at least for the time being, but pleads with Doggett to make sure the rig stays down. For as little as he likes Mulder, Doggett surely tried to do that, as he's definitely a man of his word.
It would appear that the rig's destruction might've washed away the last vestiges of the black oil, and as established in 2016's season 10, the aliens eventually abandoned their colonization plans over concerns of Earth's depleting natural resources. Considering the general resiliency and hard to define properties of the black oil substance though, it's hard to imagine it being fully and entirely wiped out. Considering The X-Files looks unlikely to ever return for a third season though, at least not unless Gillian Anderson decides to return as Scully, the black oil may be dead by default, in the sense that there's nowhere for it to be seen. Of course, that doesn't mean the black oil can never appear again in one of the many X-Files multimedia tie-ins, such as books, comic books, or video games.