Conduit

Lake Okobogee, Iowa. A teenage girl called Ruby mysteriously disappears while out camping with her mother and little brother. The case strikes a chord with Mulder, who finds parallels with his sister Samantha's disappearance 21 years ago. He and Scully go to investigate in Lake Okobogee in a bid to find out what happened to Ruby and in the process also see if the case will provide answers about Samantha's fate.

Tropes:

• Actually Pretty Funny: While Mulder knows Scully is trying to get him to admit his hunch on following a story from a tabloid is wrong, he does smile a little when she compares his case to another tabloid story about a "one hundred-year-old lady with a lizard baby."
• Armor-Piercing Response: When it seems Mulder is determined to continue with the case even after it seems it's been solved, Scully is able to make him stop.
  Scully: Mulder, stop! Stop running after your sister!
  Mulder: (Freezes)
  Scully: This won't bring her back.
  Mulder: Come with me or don't come with me. I'm not giving up until I find that girl.
• Bait-and-Switch: Kevin approaches a bright light in the forest. The light grows brighter and brighter...but it's not a UFO, it's a very large motorcycle gang on a joy ride.
• Bittersweet Ending: With more emphasis on "bitter" than "sweet" for the main characters. Ruby is returned, but her mother — fearing that Ruby will be ostracised for her experiences the same way she was — refuses to cooperate further with the investigation. Mulder is left with no answers regarding what happened to his sister, and is last seen crying in a church.
• Call-Back: When prompted, Scully tells her superior what Mulder told her about his little sister's disappearance. Said story was told to her during Mulder's Opening-Up Moment in the first episode.
• Connected All Along: In universe; Mulder points out that Ruby's mother was one of the first people to report a UFO sighting in Lake Okobogee, as she was in the Girl Scout troop that saw it while on a camping trip.
• Cynicism Catalyst: Inverted. Samantha's abduction is definitely the formative event in Mulder's personality, but if anything it has made him more willing to believe in the supernatural, as opposed to making him jaded and cynical.
  "You know, when I was a kid, I had this ritual. I closed my eyes before I walked into my room, because I thought that one day when I opened them my sister would by there. Just lying in bed, like nothing ever happened... I'm still walking into that room, every day of my life."
• Devil's Advocate: Mulder calls attention to a flying saucer tattoo on a bartender's arm and gets a little local lore on Lake Okobogee by saying people who believe in aliens are "howling at the moon".
• Friendship Moment: While she knows her superior has every reason to dismiss Mulder's proposal that a tabloid story be added to the X-Files (despite having minimal evidence that it is so), Scully stops him and suggests she learn more about Mulder's reasoning, with her recommendation being what approves or scraps the case.
• Friend to All Children: Mulder, as seen in the way he can strike up a conversation with the taciturn Kevin.
• Good Cop/Bad Cop: Mulder and Scully pull this off, with Scully as the polite but firm Good Cop and Mulder as the theatrical Bad Cop. Funnily enough, the one actual cop in the room is just sitting in the back, watching.
• Harmful to Minors: Whatever Kevin saw happen to his sister has clearly messed up his brain a bit.
• It's Personal: Ruby is abducted in a very similar way as Mulder's sister Samantha was, 21 years earlier.
• Manly Tears: Mulder is shown crying in a church after his attempts to find out what happened to his sister fail.
• Minor Crime Reveals Major Plot: Downplayed. Mulder finds and possibly solves a homicide case that reveals a very minor clue towards the X-File case.
• The Mountains of Illinois: Even by X-Files standards, this trope hits pretty hard here. The real-life Okoboji Lake in Iowa has no surrounding hills, much less forested mountains.
• Mysterious Informant: Tessa, even though this is a Red Herring as far as the main plot goes.
• Police Are Useless: Zig-zagged. While the sheriff's refusal to investigate Ruby's mother's claims seems callous, it's actually reasonable: Ruby had a history of bad behavior (having had multiple boyfriends and had run away on at least one occasion) and the police have very little reason to believe that aliens are involved. When Greg's body is found in the woods, the sheriff takes it very seriously and helps find Tessa.
• Red Herring: The coded messages Kevin's getting transcribed as 1s and 0s get mistaken for binary code revealing complex computer images and files. He's really drawing them out into a massive image of his missing sister's face.
• Room Full of Crazy: Kevin spends much of the first half of the episode writing lots of 1's and 0's onto page after page of ordinary writing paper.
• Single-Issue Psychology: Samantha's abduction is depicted as the event that has shaped almost every aspects of the adult Mulder's personality.
• Stealth Hi/Bye: After Tessa tells Mulder and Scully that Ruby got pregnant off her boyfriend, the agents are startled by a lady dropping a book. When they turn around, Tessa's gone.
• To Be Lawful or Good: Contrasted between Scully and Mulder. Scully doesn't hesitate to report 8-year-old Kevin to the NSA Agents when he is found inscribing top-secret coded messages, whereas Mulder is appalled at how awful it must be for the boy to be in custody.
• Troubling Unchildlike Behaviour: Ever since the night of his sister's disappearance, Kevin's been drawing rows and rows of 1s and 0s while sitting in front of a static TV. It turns out that he's been receiving signals from outer space, one of which is about Ruby.
• Wham Shot: One of the best examples in the entire series run. Kevin has been spending an awful lot of time writing lots and lots of 1's and 0's on ordinary writing paper. Late in the episode, Mulder and Scully come to the family's house to check up on them. They find the house empty and the papers of 1's and 0's laid out on the living room floor. Scully climbs the open staircase to check the second floor... then happens to look back down at the first floor. She calls Mulder to come up and stand beside her, and they both look down at a huge square of papers covered with 1's and 0's that form a portrait of the missing Ruby.