Dr. Paul Farraday, a biologist, and Dr. William Bailey, a member of the U.S. Forestry Service, debate the cause of a rapid decline in the frog population at Heuvelmans Lake in Georgia. Shortly thereafter, while walking near the lake's shore, Bailey is attacked and killed by an unseen force.
     Mulder and Scully drive to the lake after Bailey becomes the second person reported missing from the area in the same week (Scully brings her dog, Queequeg, along for the ride). Mulder suspects the disappearances are linked to Big Blue, a legendary, Loch Ness-like monster that allegedly lives in the murky water.
     It becomes apparent that the creature's supposed existence is responsible for most of Lake Heuvelmans' tourism business. While speaking with Ted Bertram, owner of a local tackle shop, the agents encounter Ansel Bray, a Big Blue expert who has devoted his life to photographing the elusive behemoth. The conversation is interrupted when a local fisherman barges into the shop with news that he discovered a body floating in the lake.
     The body is identified as Scott Woosley, a Boy Scout leader who disappeared after he wander from his troop to relieve himself. Scully notes that Woosley's fly is open, a common identifier of drowning victims who consumed too much alcohol and fell into the water while urinating. But Mulder believes the creature is responsible for the death.
     The agents interview Farraday, who quite openly scoffs at the notion of the existence of Big Blue. Shortly thereafter, Ted Bertram is killed by the unseen creature.
     Aided by Sheriff Lance Hindt, the agents search the area where Bertram disappeared. They inspect giant three-toed footprints imbedded in the muck on the lake's shore. But the evidence is dismissed when a "dinosaur boot" is uncovered near the scene.
     The body count increases after a teenaged diver is killed. Based on a preliminary examination, Scully attributes the death to a motor boat propeller. Not long afterward, Ansel is also attacked and killed.
     Mulder begs the Sheriff to close down the lake before anyone else is attacked. Hindt refuses, citing a lack of manpower. But as Hindt is dragging the lake for bodies, something grabs hold of his line and yanks him into the water. Immediately, he orders the lake closed.
     Scully gives chase when Queequeg suddenly darts off into the woods near the lake. She discovers the tattered remains of a leather dog collar.
     The agents rent a boat, and using a depth finder, embark on a nighttime hunt for the elusive creature. Something tears a hole in the boat's hull, causing the vessel to sink. Surrounded by darkness, the pair take refuge on a tiny rock island. But Farraday emerges from the darkness and informs the agents the shore is only a stone's throw from their island. Embarrassed, Mulder and Scully walk to shore.
     Mulder takes interest in Farraday's bag full of frogs. He realizes that the monster's sudden attack on humans was provoked by a change in the lake's ecosystem. Farraday becomes the creature's next victim, but he escapes with a flesh wound. Mulder tracks the elusive culprit through a marsh area, firing several rounds from his pistol. What he encounters, however, is a monstrous alligator, now bleeding from gunshot wounds.
     But somewhere in the lake, a serpentine form undulates in the murky, moonlit water.