Mulder and Scully investigate a strange double murder in which the victim's skeletons are found in an open field.

A man and a woman return home after a day of hiking and argue - he left her behind by walking faster. Her head hurts and while showering she has memory flashes about being covered in goo. Later, in bed, they snuggle together, and the scene transforms to two skeletons in the same position, outdoors.

Mulder and Scully discuss the skeletons of Wallace and Angela Schiff, missing only a few days. Dental records show positive ID. Scully speculates about a ritualistic killing with the bodies boiled to remove all tissue. Mulder says the bodies were found on Brown Mountain, North Carolina, where mysterious lights have been seen floating above the mountain for hundreds of years. They go to North Carolina and examine the remains. There is some yellow goo on some of the bones, like we saw Angela remember. Scully examines the skeleton while Mulder goes to the field where the bodies were found. He sees a man who appears to be Wallace and chases him into a cave. Mulder catches up with Wallace, who claims to have been abducted by aliens. A bright light shines into the mouth of the cave and Angela appears. She has a classic abduction story, except Mulder can't figure out the skeletons, which have no precedent in other abduction reports. The bright light returns and he walks into it.

Scully determines that the goo is some sort of plant-based digestive secretion. She hurries out to find Mulder, and as she follows his footprints she steps on some mushrooms that release spores. She follows him to the cave but it is just a shallow hole and he is not inside, so she leaves. Back in Washington D.C., Scully receives an urgent call from Mulder to come to his apartment. He brushes off questions about why he returned from North Carolina without her because he has Wallace and Angela there with him. In his bedroom he also has a shy little grey alien, who communicates with him and Scully telepathically. Mulder says when he was abducted he abducted the alien in return. Scully is astounded and completely convinced, which surprises Mulder. His head hurts and the room distorts. He is still in the cave, covered with goo.

Scully returns to the cave with the local medical examiner. There is goo seeping out of the ground and now there are tracks leading both in and out of the cave. A short distance away they find a skeleton which dental records eventually show is Mulder's. The medical examiner disturbs Scully to suggesting the identical ritualistic killing scenario she proposed to Mulder. In Washington, she talks with Skinner and is surprised that he accepts her report, since it had no answers. She realises that her scientific explanations rarely explain X-Files. She goes to Mulder's apartment and finds a wake in progress. The Lone Gunmen are there and many other people, including a couple of men in traditional Jewish garb standing near the coffin. Scully is disturbed that the Lone Gunmen accept the murder theory without question. They should be "all over this" as something that has a hidden cause. Scully ends up screaming, "what have you done with him?"

Mulder knocks on the door and when he enters his apartment, all of the other people disappear. He tells of being abducted, but he cannot answer her questions -- even about why he knocked on his own apartment door. Scully concludes that it is all an hallucination and that the mushroom spores in the field are causing it. What if the mushroom and the goo are from the same organism and they are still in the cave, and the organism needs to feed on flesh? It could be digesting them right now. Mulder struggles out of the soil and pulls Scully after him. Later, they report to Skinner. The organism extends for at least ten acres underground and the spores have a structure similar to LSD. Skinner comments that it is a rare day when Mulder and Scully both agree on the explanation of an X-Files. That makes Mulder wonder. He doesn't understand how they escaped. He asks Scully to name one other drug that loses its effect when the person realises he is drugged.

To prove they are still drugged, Mulder pulls out his gun and shoots Skinner. Goo comes out of the bullet holes. They are still underground. Mulder begins struggling, although he presumably can't see where he is. His hand reaches above the soil and he is found by a search part lead by Skinner. They are all wearing air filter masks - apparently because one of the tests revealed the action of the spores. Mulder and Scully are pulled out of the ground and loaded into an ambulance. They hold hands as they are driven off.