Despite orders to stay away from the X-Files, Mulder finds himself stranded on a quarantined oil rig with Doggett where the crew have been infected by an alien virus that Mulder has encountered many times before.
On the Galpex-Orpheus Platform in the Gulf of Mexico, the oil workers are watching hockey after a hard day’s work. One worker slips away and goes to the radio room. He stabs the radio man with a knife stolen from the kitchen. When the television reception goes on the blink, the crew chief goes to find the communications officer to get him to fix it. Finding the worker who slipped away smashing up the equipment in the communications room, he pushes the man into the wall and turns over the corpse of the comms officer. Black oil crawls under the comms officer’s skin and pools in inky darkness within his eyes. The crew chief traps the worker in the room and faces him. The glow starts in his eyes as it spreads over the man’s body and intensifies while the worker screams in terror.
Agent John Doggett arrives at the X-Files office and finds Agent Fox Mulder looking through the files. Mulder, no longer assigned to the X-Files, questions why Doggett is not pursuing the death of an oil worker found horribly burned with charring consistent with exposure to high levels of radiation. Doggett recognizes that Mulder is referring to incidents of the “black oil” in the X-Files. Sarcastically, he recounts that it is supposedly an alien virus key to the conquest of Earth and that the virus can take over a person’s body and mind. Doggett believes this burned oil worker and the missing communications officer were merely the victims of a natural gas explosion as the oil company claims. Agent Dana Scully calls the office and tells Doggett that Deputy Director Kersh demands to see them because someone from their offices supposedly called the oil company.
Mulder and Doggett both go up to the meeting because clearly Mulder called them and misrepresented himself as part of the X-Files department. Mulder apparently stirred up a hornet’s nest by implying the FBI was launching an investigation into the death of the Mexican worker, Simon de la Cruz. A Vice President from the oil company, Martin Ortega, explains that the oil platform discovered a vast new oil field but it extends far south into Mexican waters. The Mexican government would like to use Simon’s death as an excuse to claim the new field for themselves. Now, Kersh will have to launch a criminal investigation to confirm no wrongdoing and will send Doggett.
Doggett arrives on the platform via helicopter with the new communications officer, Yuri Volkov. The manager, Mr. Saksa, meets him but is confused since they heard only one agent was being sent but another arrived that morning. Mulder is already there and meeting with the crew chief, Bo Taylor, about the incident. Doggett is ticked off at Mulder but Mulder insists he sit down and listen to the crew chief so he won’t have to repeat his story. Taylor tells them that Simon de la Cruz went mad out there, like some people do stuck on a rig for long durations, and he tried to blow up the rig; the communications officer was on the drill floor taking a walk and was caught in the explosion.
Doggett says he could call Kersh but he won’t as long as Mulder follows his lead. Mulder assumes Doggett will not be able to find anything but Doggett immediately realizes the crew chief was lying through his teeth; that he knew what really happened. Mulder agrees and suggests other people know as well.
Scully talks with Assistant Director Skinner about the autopsy she conducted on Simon de la Cruz. She reveals that the man had the “black oil” alien virus in his brain but the virus was dead for an unknown reason. She asks Skinner to tell Kersh that they need a forced evacuation of the oil rig but Skinner says there isn’t enough evidence.
The new radioman, Yuri, tells Taylor that there’s some sort of high frequency interference on the radio system that seems to be an incoming signal. He needs to power down to fix it, but Taylor disagrees and infects the man with the black oil.
Scully calls the rig on the radio and is surprised to get Mulder; she tells him about the situation and he passes it onto Doggett who has the rig quarantined.
Mulder and Doggett ask Mr. Saksa, manager of the rig, about a missing deckhand, Diego Garza. Saksa notices the man is indeed gone and says Garza was a friend of de la Cruz.
Skinner and Scully meet with Ortega in the morgue and he doesn’t think the crew is infected. He plans on having that crew go home and a new group sent over.
Mulder hypothesizes that the new oil field is infected with the alien virus and this oil could be used to infect the entire oil consuming world. An alarm draws them to a fire in the radio room, but when Doggett goes to find another fire extinguisher, Diego Garza knocks him unconscious and takes him to wherever he was hiding.
Kersh confronts Skinner and Scully about being kept out of the loop on this autopsy and the quarantine of the rig which he learned about through Ortega. Skinner accepts responsibility for the quarantine and Kersh demands that the quarantine be lifted. Scully tells him that they have lost radio contact and would have to wait until it is reestablished.
Mulder tries to contact Doggett but Doggett is being held captive by Garza. Garza cuts Doggett to confirm he has red blood; through him Doggett learns that Garza set the fire, that de la Cruz was murdered by the oil workers, and that the radio is being used to contact the “flying ships.” “Vienen!” “They’re coming?”
Scully illuminates Skinner about de la Cruz. He had an extremely high T-cell count, due to his genetic background as a Waicha Indian, which made him a “virus fighting machine” so he was irradiated by the crew because the virus didn’t work on him.
Doggett convinces Garza to let him go and promises that he will get Garza home to his family. When Doggett leaves he promptly runs into Taylor who demands to know Garza’s location. He tries to infect Doggett, revealing the black oil eyes to the skeptical Doggett, but Mulder knocks out Taylor. They retreat into the radio room as the oil workers siege the room.
Doggett repairs the radio enough to contact Scully. Doggett explains about there being only three uninfected people who need evacuation and describes Garza as mentally unstable due to attacking of the radio room out of the belief that they are contacting alien ships via radio. Mulder realizes that Garza was right about them using the radio to contact the ships. He smashes up the radio and notices that the siege has stopped. They leave the radio room and find no oil workers anywhere nearby.
Doggett insists on finding Garza and getting him out too. He returns to where Garza was hiding. Mulder says, “Is he coming?” Doggett turns the body of Garza finding him covered with radiation burns.
They run out of there and find out why the workers disappeared. They have been damaging the rig and the whole place is going to explode. The black oil victims stare at them as they are cut off from Doggett and Mulder by falling debris. The two FBI agents leap from the platform to be rescued by the helicopter that has arrived.
Doggett is looking for files pertaining to the oil rig incident to bring to his report to Deputy Director Kersh but Mulder stops him. He tells Doggett that the ringing phone is Kersh calling to say that blame has been assigned. For going to the platform himself without any orders sending him there, Mulder has been blamed for everything that happened there. Mulder tells Doggett he should do everything in his power to make sure they don’t drill that oil. Kersh has happily dismissed Mulder from the FBI in the wake of Galpex Oil losing the right to drill oil in that entire region.
Mulder accepts the fall to protect Doggett and the X-Files. He reminds Doggett that he saw the black oil in people’s eyes there, that he knows the truth now. He passes the X-Files on to Doggett recognizing that the man has given the offices a renewed credibility and that Doggett has Kersh’s ear. “Answer the phone, Agent Doggett. You’re in charge here now.”
- "Vienen" is Spanish for 'They Come'.
- This is the final episode to feature the nefarious black oil.
- This is the final episode in which Fox Mulder is officially an FBI agent until the Season 10 revival.
- The final scene is the last time Mulder is seen in his basement FBI office until the 2016 episode "My Struggle".
- David Duchovny as Special Agent Fox Mulder
- Gillian Anderson as Special Agent Dana Scully
- Robert Patrick as Special Agent John Doggett
- Miguel Sandoval as Martin Ortega
- Casey Biggs as Mr. Saksa
- Gregory Norman Cruz as Diego Garza
- James Pickens, Jr. as Deputy Director Alvin Kersh
- M.C. Gainey as Bo Taylor
- Lee Reherman as Yuri Volkov
- Luis Villalta as Simon de la Cruz
- Kevin C. Loomis as Chef
- Steve Wilcox as Ed Dell
- Rich Marotta as Hockey Announcer