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Finish Dialogue in Unison: Mulder talks about Ahab and his wish to have a peg leg, and shares his favourite line, which they finish in unison.
Scully: And that's not flippant?
Mulder: No, flippant is my favourite line from Moby Dick. Hell is an idea...
Mulder and Scully both:...first born on an undigested apple dumpling.
Infant Immortality: Averted with Queequeg. Scully's Pomeranian was eaten by the monster. In fact, it was an alligator. Probably.
Inspirationally Disadvantaged: Invoked by Mulder, who claims to have always wanted a peg leg on the grounds that if he were disabled, just getting through everyday life would be enough of a heroic accomplishment that he wouldn't feel compelled to spend his life obsessively questing for the Truth.
Mister Muffykins: Mulder is not pleased that Scully took her small dog Queequeg.
Moby Schtick: The biggest Shout-Out to Moby-Dick that appeared on the show. When Scully's dog Queequeg (named after the harpoonist) dies, Scully talks about the book as her favourite since she was little, and she reminiscences about her father reading to her from it. She compares Mulder's self-destructive obsession with his quest to Ahab's white whale. Mulder and Scully even share a favourite quote, which they recite in unison: Hell is an idea first born on an undigested apple dumpling.
Mundanger: The thing responsible for the killings is not Big Blue the sea monster, but an alligator.
Not the Nessie: Mulder went after this case to prove that a lake serpent was responsible for the numerous deaths. He's disappointed to find out a dangerous alligator.
Stock Ness Monster: Mulder and Scully investigate reports of a lake serpent and find a surprisingly ordinary, albeit still deadly, alligator. This being The X-Files, however, after they've left, The End... Or Is It? ending shows there really is a serpent in the lake.
Dude: "Saw this, you know on the Discovery Channel. They got like this, you know, cult built up around these toads. The skin's got these, hallucinogenic properties. Lets you see all these visions. It's really spiritual. It's supposed to take the doors of perception, and swing them so wide open, you know, plus you get to see all these cool streaks and trails and crap." *licks the toad*