There's a murder on an oil rig... but is the oil what it seems?
Ed Dell, the communications officer of the Galpex-Orpheus oil rig is stabbed by a crewman, Simon De La Cruz. At the same time, the television in the rig's mess hall dies. Bo Taylor, the crew chief, investigates the communication shack to discover Ed Dell's body, which has something moving beneath the skin. Simon tries to escape, but Bo knocks him down - when his body starts to glow.
Mulder visits Doggett to tell him about the murder - the victim had 90% burns on his body which seem to be radiation burns, not caused by an explosion as the oil company claims. Mulder thinks it may be due to black oil.
Mulder and Doggett meet Mr. Ortega, the Galpex Petroleum VP in Kersh's office. Galpex have found a huge oil reserve in the Gulf of Mexico, which Ortega thinks Mexico may claim. Kersh sends Doggett to investigate, but when he arrives, Mulder is there before him.
They meet Bo Taylor, who claims Simon went beserk and tried to blow up the rig, killing Ed Dell. Scully, however, finds Black Oil in his skull during an autopsy - but it's dead, as if irradiated.
On the rig, Yuri, a technician, tries to fix the rig's radio but is attacked by Bo and spattered with Black Oil. Yet when Scully speaks to Yuri he seems unaffected. Scully tells Mulder about Simon's oil infection, and Mulder urges her to find a way of fighting the infection.
Doggett and Mulder quarantine the rig, but one crewman is missing - Simon's friend Diego Garza. Ortega the VP threatens to change the crew unless the agents can proove the infection exists. Doggett and Mulder search for Diego, who is a mestizo like Simon. Perhaps he saw something that has sent him into hiding?
An alarm sounds - the communications shack is on fire. As the agents tackle the fire, Diego attacks Doggett, knocking him out. Regaining consciousness, he finds Diego cutting his arm to check for black oil. Despite his limited Spanish, Doggett realises that Diego set the fire because 'they're coming'.
Meanwhile, Kersh tells Scully that he is lifting the quarantine, against her advice. Scully realises that Simon is a Huecha Indian, and possibly immune to the Black Oil. Whilst the virus didn't kill him, radiation burns did.
Simon lets Doggett leave. Doggett finds Bo, tells him that Diego is alive, and is attacked. Just as he is about to be infected with Black Oil, Mulder helps him overpower his attacker. The agents barricade themsleves in the communications shack, and try to relay a message, whilst the rig crew surround them.
Scully gets though to the rig, and tells Doggett and Mulder that the new crew are on their way by helicopter - Kersh has broken the quarantine. Mulder destroys the radio - so the rig workers can't contact other aliens. The rig workers stop their attack.
Making their way outside, Doggett goes to rescue Diego - finding him burnt in the bowels of the oil rig. He rejoins Mulder, and they head for the production deck. Pipes start bursting, and fire breaks out as the helicopter arrives. Unable to land, the pilot tells the agents to jump. As they hit the water, the rig explodes.
Back in the bureau, Doggett tells Mulder that Kersh blames him for the rig disaster, and has thrown Mulder out of the FBI.