Black Oil infects oil rig workers except two. They belong to the Huichol, a genetically pure Mexican tribe that is naturally immune to the Black Oil. Mulder disobeys orders and investigates on his own with Doggett. The oil rig ends up exploding. Kersh fires Mulder from the FBI; Mulder hands in the X-Files to Doggett.
'Vienen', spanish for 'they are coming'. Written by Steven Maeda, not a mythology regular, but successfully playing with traditional mythology elements: the Black Oil and its radioactive properties, something not touched upon since season 3! And also introducing elements of that traditional mythology that were not revealed when they were initially planned to be: the natural immunity to the Black Oil. The X-Files crew gets to play with an oil rig! Helicopters! Fires! Explosions! Mulder and Doggett jumping off the rig action movie-style!
The Orpheus oil rig
Mulder theorizes that the workers want to produce and spread the Black Oil deposit so that it infects more people. Given how oil-dependent we are, that should be easy, however we know that another means of spreading the Black Oil has been designed: bees (Fight the Future). Instead, the infected workers are emitting a signal to contact the Colonist ships -- a signal interpreted as nonesense interference by the communications officer: "there's some sort of high frequency interference that I have no idea how to get rid of [...] filtering in across a large range of channels" -- probably expecting to be picked up. In the end, the infected workers themselves blow up the oil rig, perhaps in an attempt to seal the oil deposit for good as it had attracted too much attention with Mulder and Doggett. The workers die, but the Black Oil must have survived, returning to a dormant state, waiting for the colonization. In the aftermath, "Galplex has lost the right to drill that entire Texas oil province".
Immunity to the Black Oil
Not all of the crew was infected, however. The only two Mexican nationals were not. Somehow, the Black Oil that entered them died. Both of them knew what was going on, knew that "they are coming" ("ya vienen") in their "flying saucers" ("platillos voladores"). Simon de la Cruz and Diego Garza tried to resist the infected workers, by sabotaging the rig and by destroying or setting fire to the communications station that was the rig's link to the mainland. Simon was discovered and one of the infected workers, as he could not make him one of their own by infecting him, killed him with a radioactive flash ("the crew members who were affected by the virus couldn't control him, so they killed him, by irradiating him") -- these "radioactive properties" were already seen in Piper Maru. Simon's body was thrown to the sea and Diego went into hiding.
What was so special with Simon and Diego? They were listed as Mexican nationals, as "mestizo", which is spanish for person of mixed descent ("mixed Mexican descent"). Scully determines that they were in fact Huichol Indians (Scully actually says "Waicha" but to the best of my knowledge this is an invented term; in the subtitles, she says "Huichol", who are a very real people). "The Huichol are an indigenous Mexican culture that has a rare undiluted gene pool." Indeed, the Huichol were independent of the Aztec rule of Mexico, and later gave trouble to the newly created Mexican state with claims for independence; cross-breeding must have been scarce, and genetic traits must have survived through the generations. This is common to isolated cultures.
The Siberian connection part II: migration
Had this "genetic immunity" been discovered earlier by the Syndicate, the search for a successful hybrid would have been shortened by decades! By transferring just the gene in question, one could become immune. Better yet, this genetic immunity could have become the basis for providing the necessary antibodies and creating a vaccine against the Black Oil.
Mulder passes the torch
This is the only episode where Mulder and Doggett are teamed in an investigation (one could count 8X19: Alone as well). For much of the episode, Mulder is a hinderance slash pain-in-the-neck to Doggett. Mulder is not assigned to the X-Files so he acts on his own, like his old obsessive self, in order to investigate 'his' Files. Doggett tries to be in charge, to control Mulder ("We're going in one direction. My direction.") but he quickly learns that's impossible. This trial by fire (literally) will allow for Doggett to gain Mulder's trust. He has now seen the enemy, he knows what to fight against: "you have seen it now, out on that platform. You saw it for yourself." Mulder's fate in the Bureau was dangling by a thread already; this last case, where he abused his authority as an FBI agent to investigate without clearance, allowed Kersh to finally give him the final blow ("the blame has been properly assigned"). Mulder is taken off the X-Files and is taken off the FBI altogether. Mulder shakes Doggett's hand and leaves the X-Files office, the office he's had for ten years, for good. "You're in charge here now."
Doggett: "Five years ago, you and Agent Scully investigated a case of a World War Two plane salvaged from the bottom of the Pacific Ocean, where a sepsis was brought to the surface which you describe as a highly contagious virus of extraterrestrial origin that has radioactive properties and can take over a man's body and it's part of an alien conspiracy to colonise the planet, if I'm not mistaken."
Mulder: "And you'd love to help, but you left your lightsaber at home. (pause) How'd you get stuck down here, Agent Doggett? Did Kersh catch you peeing in his cornflakes?"
Doggett: "I never would have believed it. These stories about you."
Mulder: "Really? What stories are those?"
Doggett: "That you can find a conspiracy at a church picnic."
Mulder (promptly): "What church?"
Scully: "And what if I can't?"
Mulder: "When he's old enough, tell the kid I went down swinging."
Diego Garza: "Confio en nadie." [I trust no one]
Mulder: "You're all the credibility this office has left. You have Kersh's ear and you have seen it now. Out on that platform. You saw it for yourself. (phone rings, it's Kersh) Answer the phone, Agent Doggett. You're in charge here now." (Mulder shakes Doggett's hand and walks out the X-Files office for good; the phone keeps ringing as Doggett looks at it)