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.
- 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 the mother 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.
- Creepy Child: Kevin, even though he is sweet enough when Mulder talks to him.
- 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.
Mulder: 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.
- Friend to All Children: Mulder, as seen in the way he can strike up a conversation with the taciturn Kevin.
- 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 at the Downer Ending.
- Masculine Girl, Feminine Boy: This episode is probably the first time we get to see how Gender Inverted the Mulder-Scully pairing really is.
- Minor Crime Reveals Major Plot: Inverted, in a way. Mulder finds and possibly solves a homicide case that reveals a very minor clue towards the X-File case.
- Mysterious Informant: Tessa, even though this is a Red Herring as far as the main plot goes.
- NSA: NSA (No Such Agency) Agents break into Mulder's hotel room.
- 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.
- Single Issue Psychology: Samantha's abduction is depicted as the event that has shaped almost every aspects of the adult Mulder's personality.
- 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.