In a small town, Mulder and Scully investigate rumors of a prehistoric lake monster called Big Blue.
Mulder and Scully investigate a missing person case after Dr. Bailey's body disappears at the edge of a large lake. Apparently, he and another scientist, Dr. Faraday, had a heated discussion, in which Dr. Faraday said Dr. Bailey that nature should be preserved (frog population was down), not only for future generations, but also out of respect. Nature is dangerous. Scully brings along her dog, Queequeg, because of the Mulder's hasty schedule. In his case debriefing, Mulder tells Scully about the case of another missing person, involving a Boy Scout leader. Scully wonders why a missing person's case would attract Mulder's fascination, until she finds out that the place is the home of a legendary lake monster called "Big Blue."
Mulder and Scully then ask the local bait shop what they believe in this tale. The locals enjoy the publicity because it brings tourists like them. A local man makes it his priority to photograph Big Blue and make a movie. Despite his persistent efforts to do so, and out of the hundreds of photos taken, he has been unsuccessful.
The Boy Scout Troop Leader's body then resurfaces, or at least half of it. Mulder and Scully discuss nature, saying that while we may eat them, they, ultimately, eat us. The halved body is still not enough evidence for Scully. She believes that a possible propeller in some kind of boat could have done that much damage. Even if it didn't halve the man, he would have been finished off by the nibbling/ biting of local fish. "Were they saving the other half for later?" Mulder asks. On the contrary, Mulder believes that this "mystical" creature is a prehistoric dinosaur. It has been attacking people because it is being forced to protect itself from colonization; not alien, from locals. The frog population was also dying out, meaning that the creature was being driven into the woods to find alternative food sources; the water was being polluted and being used more by people.
The two then decide to have a little stake-out. While Mulder looks through all of the pictures taken by the determined local, Scully takes Queequeg out for a walk. Unfortunately, it was his last. Scully never did see what bit through the dog's leash and took him away. Mulder, being as sympathetic as he can, decides to go out for a boat ride and quench this mystery once and for all.
While driving the boat, Mulder notices something on radar: it's big and fast, coming straight for them. Whatever was in the water crashed into the side of their boat, forcing them to abandon ship. They rest of a rock out in the middle of the lake, thinking that they're miles from shore and that the water is too deep. While sitting there, Mulder and Scully have a meaningful conversation. Scully talks about her dad and his respect for the sea and nature, and Mulder delves into his beliefs of cannibalism and life. Scully compares Mulder to Captain Ahab, being so driven to find the answer that it will destroy his life and ultimately kill him. Mulder doesn't notice the criticism, but rather how Scully is able to know and list everything about him through the analogy.
Dr. Faraday discovers them sitting on the rock, but they're fairly close to shore. Later on, Faraday is attacked by something in the woods. He is hurt, but does manage to survive. Mulder races after the creature despite Scully's pleas. The creature surprises and charges Mulder, who empties his gun into it before it finally dies. The creature turned out to be an alligator, of all things. Disappointed, he and Scully have one last look at the lake. Scully tells Mulder that there are more mysteries out there to be solved, and that just because this adventure didn't support his theory, he shouldn't give up. As they turn away, the real Big Blue, indeed a plesiosaur-like creature, rises up from the water to watch them before diving back down below the surface, unnoticed by either Mulder or Scully.
- This episode marks the final appearance of Scully's dog, Queequeg, which was previously seen in "Clyde Bruckman's Final Repose" and "War of the Coprophages". In a 2013 "Ask Me Anything" forum on Reddit, Gillian Anderson joked (or perhaps not) that she was not sorry to see Queequeg go: "That dog killed people with its farts and it deserved to die a nasty death in the mouth of that alligator or whatever it was. Ugh. I had to shampoo it, or walk away every few seconds, because these puffs of nastiness kept happening."
- The characters "Stoner" and "Chick", played by Tyler Labine and Nicole Parker, first appeared in "War of the Coprophages."
- Darin Morgan reportedly made uncredited contributions to the script (particularly the conversation on the rock), hence there are several references to his previous Season 3 episodes.
- Sky Television mentioned Queequeg's death in their synopsis of this episode.
- Heuvelmans Lake was actually Buntzen Lake, just north of Coquitlam, BC. The map of the lake used by Mulder is an actual map of Buntzen.
- In X-Files:Resist or Serve, a Quagmire Movie poster can be found at Wetwired Video in Red Falls Colorado. Apparently somebody used the events of Quagmire to make a movie.
- This is the only episode with correct, real world uniforms and logos in reference to the U.S. Forest Service.
Cast and Characters
- Timothy Webber (Dr. Paul Faraday) previously played Detective Talbot in The X-Files episode "Tooms" and Jess Harold in "Our Town".