- The skeletal remains of a young couple are found after they have been missing for only three days in an area known for UFO activity. Mulder and Scully have different experiences in the investigation but nothing is quite as it seems.
- A young married couple's skeletons are found together on a field in the mountains after only being reported missing for three days. The area where their skeletons were found is known for UFO activity, so Mulder and Scully go there to investigate it. Mulder finds the couple alive and all signs point to an alien abduction. But everything is not as it seems.—Muldernscully
- A young couple, Wallace and Angela Schiff, returns from a hiking trip; the wife is in some pain. Later, their skeletons are found locked in an embrace in the woods.
Mulder points out that the location where the bodies were found is associated with UFO activity.
The agents go to examine the skeletons, which have been confirmed by dental records to belong to the couple. Scully remains behind to check out some organic material on the bodies, while Mulder drives to the crime scene. He identifies the same organic material, a green sludge, that Scully found. Then he sees Wallace Schiff walking by, and chases him into a cave.
The sludge turns out to be a digestive acid. The doctor gives Scully some old case files with similar skeletal remains, and she goes to find Mulder.
Mulder chases down Schiff in the cave. He says the skeleton is fake, and that he and his wife were abducted by aliens. They kept his wife but returned him. The two begin hallucinating and they run and hide when a bright light appears at the cave's entrance. Deeper in the cave, they find Wallace's wife. She confirms the abduction story, and Mulder realizes she has been implanted with a probe. He takes them back to Washington secretly, calls Scully to his apartment, and shows her an alien that Mulder has managed to capture. But after seeing green sludge coming from his tap, the scene wavers, and Mulder awakens back in the cave, covered in sludge.
Scully arrives at the cave with the doctor, where they find footprints leaving the cave and a new skeleton. Dental records show that it is Mulder's. Scully suggests the green sludge was responsible, but there is no sign of it on the skeleton. The doctor suggests that a ritualistic murder is a simpler explanation. Skinner agrees when she discusses the case with him, but Scully still has doubts.
Afterward, she goes to a wake at Mulder's apartment. The Lone Gunmen are there and they tell Scully they will help find the murderer. Skinner tells her she should go home, then the scene wavers as someone knocks on the door. She goes to open it; it is Mulder and everyone else has disappeared.
Scully and Mulder discuss the case. Scully suggests they are currently hallucinating after inhaling mushroom spores at the scene of the crime. The scene wavers. Scully disappears.
They pull themselves from out of the ground. Later, they report to Skinner, and confirm a mushroom extending over ten acres that uses hallucinogens to attract prey. But Mulder doubts that they've actually escaped. To prove his theory, he shoots Skinner through the heart, and green sludge comes out. Mulder disappears.
They try to pull themselves out of the ground, and a rescue team arrives on the scene. The team confirms finding the mushroom, and Scully and Mulder are transported away by ambulance as the show ends.
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