In a remote section of North Florida, two surveyors, Michael Sloan and Marty Fox, encounter a strange creature with glowing red eyes. Sloan is suddenly yanked downward, disappearing beneath the dense brush. Shortly thereafter, Marty is also attacked. While hunting for possum, twelve-year-old Louis Asekoff and his father discover Marty's abandoned surveyor's transit. Sensing something isn't quite right, the Father sends Louis home with the dog. As the boy runs home, two shotgun blasts echo through the forrest.

Meanwhile, Mulder and Scully ride with agents Michael Kinsley and Carla Stonecypher on a highway stretching through rural Florida. Their destination: an FBI creative team seminar, in which participants are required to use their imagination to perform constructive problem solving exercises (a gathering which Mulder views as a waste of time). The agents' journey comes to a sudden halt when state troopers set up a roadblock on the highway. His spirits lifted by the unexpected diversion, Mulder suddenly exits the vehicle for some detective work. Search and Rescue leader Michele Fazekas tells Mulder that several people are missing, and that a set of tracks found at the scene could not be identified as man nor animal. His interest piqued, Mulder arranges for he and Scully to lodge at a nearby motel... saving himself the torment of attending the teamwork seminar. That night, something sneaks into the Asekoff residence. A terrified Louis tells authorities he was chased by an invisible creature with glowing red eyes. Though the story is dismissed as the product of a young boy's imagination, Mulder discovers a set of tracks inside the house. Mulder tells Fazekas the creature must be found before it can do more harm. Aided by Jeff Glaser, a "tech head" who possesses an infrared tracking device, Fazekas, Mulder and Scully set out in search of the predator. During the journey, Mulder theorizes that the creature is attacking humans in response to encroaching development.

The infrared device detects two creatures in the dense brush, each moving in opposite directions. The group splits up and a chase ensues. Suddenly, Fazekas is yanked downward, and disappears beneath the undergrowth. Mulder realizes that the creatures deliberately separated the group into two units, allowing for easier access to the leader (Fazekas). As the threesome embark on a rescue mission, Mulder recounts an X-File from the early 1950s in which a town in West Virginia was terrorized by primitive-looking men with piercing red eyes. The creatures were dubbed "moth men" by local residents.

Mulder, Scully and Glaser accidentally stray from the marked trail. Their journey is interrupted when the mysterious creatures make another appearance. Guided by directions from Glaser and the infrared device, Mulder ventures deep into the brush. Suddenly, a creature springs from its hiding place. Mulder opens fire, but the creature disappears from view. Shortly thereafter, Glaser separates from the group and he, too, disappears.

While discussing the encounter with Scully, Mulder is suddenly yanked downward. When he resurfaces, like a jack-in-the-box, Scully opens fire, shooting into the bushes nearby. Mulder goes into shock, and Scully does her best to keep him warm as darkness falls. The following morning, as Scully searches for food, she suddenly drops from view. Mulder rushes to her aid†and realizes she fell into a small cave. Inside the chamber, Scully discovers Fazekas and Louis' father, barely breathing and strapped to thick poles. When Scully realizes one of the creatures is nearby, Mulder tosses her his gun. A few moments later, when the second creature approaches, he jumps from his vantage point and lands next to Scully in the cave. One of the creatures rushes the agents. Scully opens fire, striking the predator. The agents move forward for a closer look†and realize their attacker is a man who lived like an animal. Kinsley and Stonecypher arrive and call for help. Mulder notices the words "Ad Noctum," or "into darkness," carved into one of the poles. He points out that Spanish conquistadors carved warnings on posts in the same manner... then notes that Ponce De Leon sought the Fountain of Youth in the area 450 years earlier. He concludes that the predators perceived humans as a threat to their territory, and acted accordingly. Stonecypher notes the creatures would pursue anyone who had entered the woods. Fearing the worst, Mulder suddenly rushes to Scully's motel room. He finds his partner safe and sound, and the pair leave the area. Staring out from beneath Scully's bed, however, is a pair of glowing red eyes.