A mystery involving two skeletons leads the agents on a journey in which nothing is quite as it seems.
Wallace and Angela Schiff returning home after a day out hiking in the fields of North Carolina. Angela appears to be exhausted after spending most of the day chasing after her over-eager husband and is starting to get a headache. Whilst taking a shower she thinks she is hallucinating and seeing images of a yellow gooey substance running down the walls in the shower but shakes it off. Angela and Wallace head off to bed in each other's arms but as the camera pans out we see their skeletal remains in the same position in the middle of a field.
Mulder is filling in Scully about the discovery of the remains at a well known site of strange unexplained phenomena but Scully seems keen as ever to find a more rational explanation. After showing her images of the bones and the fact they were only a few days old Scully concludes it looks like a ritualistic killing and that the bones were stripped of the flesh by boiling with/or acid. However, they head off to examine the remains themselves.
The coroner is just about to send the remains away for burial when Mulder and Scully arrive to view them. After closer examination they find a strange yellow goo covering the underside of the skeletons which was missed in the original examination. Mulder heads out to the scene of the discovery while Scully stays to perform more testing on the remains.
As Mulder arrives in the fields, he inadvertently drives over a patch of mushrooms with his car which seem to release a cloud of smoke. As he exits the vehicle and takes a look around he spots what he thinks is Wallace running away and takes chase, eventually following him down a cave. Inside the cave, Mulder finds that the way he came in seems to have been replaced with solid rock. He catches up with Wallace in the cave and discovers that Wallace thinks he and his wife Angela have been abducted by aliens who covered up their disappearance with the skeletons. Meanwhile, Scully has discovered that the yellow goo mainly consists of organic material found in digestive juices but this seems to emanate from a plant rather than an animal. Unable to reach Mulder on the phone she heads off to find him.
Arriving at the field, Scully starts to look for Mulder and accidentally steps on some more of the mushrooms that Mulder flattened earlier. Starting to follow his tracks, Scully finds they lead up to the cave and apparently lead inside.
Mulder and Wallace are now talking when a bright light appears in the tunnel entrance. Wallace is scared it's the aliens returning but Mulder heads up to take a look and finds Angela has returned from her 'abduction'. After describing the 'text book' story of the tests that have been performed as well as locating an implant, Mulder starts to believe their story. Once again, the bright light from the tunnel entrance begins to shine and Mulder heads up to investigate.
We fade to Mulder's front door as Scully arrives. Mulder answers and checks she is on her own before letting her in. Inside are Wallace and Angela and Mulder explains how they got there. Scully still doesn't believe the alien abduction story until Mulder shows her into his bedroom and hiding behind the boxes in the dark is an alien creature. Scully is astonished and quickly apologizes to Mulder for ever doubting him. However, Mulder starts to doubt his surroundings and his disbelief in what is going on begins to increase. As he washes his face with water he starts to see the yellow goo Angela saw earlier but quickly shakes it off as a dream. But then as he discusses the situation with Scully everything seems to fade away and Mulder awakes in the cave he followed Wallace into earlier, covered in the yellow goo apparently, being digested alive.
Outside in the field, Scully and the coroner happen across more of the yellow goo. The coroner also spots footsteps leading out of the cave which Scully insists weren't there earlier. However, as the coroner follows them, he finds Mulder's skeletal remains lying on the ground.
At the coroner's office, Scully is identifying Mulder's remains from his dental records but finds no evidence of the goo on the skeleton. The coroner then informs Scully that he believes that this is a ritualistic killing with boiling of the bones in an acid to remove the flesh, the theory Scully had originally believed to explain the remains of Angela and Wallace.
Back at the FBI, Scully is reporting back to Skinner about her report and her findings of the deaths of Mulder and the Schiffs. Skinner seems to agree with Scully's report but Scully is herself doubting her own findings and is not convinced by her own theories that everyone seems to be agreeing with.
We cut to Mulder's apartment and it appears that Mulder's wake is in progress. Notably, Skinner and the Lone Gunmen are in attendance along with several others. The Gunmen tell Scully they looked at her report and totally agree with her findings, Scully finds their agreement unbelievable. There is a knock at the door and Scully answers to find Mulder standing in the doorway. The rest of the wake congregation have meanwhile, disappeared. As Mulder and Scully discuss what has happened, they both begin to realize that they are both still in the cave being digested by the goo and that the mushrooms they broke caused an LSD type 'trip' causing them to become comatose whilst the organism began digesting them. As the realization occurs, they both awaken, deep in the cave and Mulder fights his way out of the ground dragging Scully behind him to safety.
We cut to Skinner's office where Mulder and Scully report on their findings, that an organism spreading many miles underground lures its prey into being consumed by inducing a hallucinogenic trip whilst it digests them. Skinner notes that this might be the first time their reports agree on the same conclusion. However, Mulder begins to doubt that they're free at all, asking Scully to name any sort of drug that causes its effects to halt once the user knows they are hallucinating, and observing that they have no apparent flesh injuries despite being exposed to the goo's hydrochloric acid. Scully is in disbelief until Mulder proves his point by shooting Skinner in the chest; the yellow goo oozes out of the bullet wounds.
Once again, their surroundings fade away as they awaken underground again in the cave. Mulder manages to stick his hand through the earth ceiling as Skinner and a team of rescue staff with masks on manage to locate them and drag them out and haul them to the safety of an ambulance. In the ambulance, Scully and Mulder hold hands.
- The small gray alien was played by seven year old Cody Weselis, son of X-Files stunt coordinator Danny Weselis.
- There is no such place as "Boone County, NC", although the city of Boone, NC, is not far from Brown Mountain. Brown Mountain sits on the county line between Caldwell and Burke Counties.
- When Angela Schiff is in the shower you can briefly see the top of her sports bra.
- In the scene just after the opening credits, Mulder is describing the Schiffs' bodies being found in the vicinity of Brown Mountain, North Carolina; on the stand next to him is a giant map of South Carolina.
- "North Carolina" is shown with desert scrub and red rocks when Mulder arrives to see Brown Mountain. In reality the location is likely California, perhaps the Malibu hills.
- When Scully approaches the area where Mulder's car was left, she is driving the coroner's pickup truck. And while the decal on the door of the truck clearly states Boone County Coroner, the truck has a US Government license plate on the front. In actuality it should have a county plate.
- In one of the final scenes, Mulder discovers that they are still hallucinating, because their skins are unmarked even though they spent several hours covered in digestive acids. Later, when they are really rescued from the acids, their skins still show little sign of being eaten at for several hours.
- After Mulder shoots Skinner; Mulder strikes the James Bond pose.
- Scully: You're saying these aliens had nothing better to do than buzz the same mountains for the past 700 years?
- Mulder: It sounds like crap when you say it.