Mulder learns the fate of his sister Samantha.
- Ascend to a Higher Plane of Existence: Implied that's what happened to all the child victims, including Samantha.
- Bittersweet Ending: Mulder finds out that Samantha along with Amber Lynn died but she seems to be happy and in a better place, wherever she is. Her apparition even hugs Mulder and he later exclaims "I am free."
- Holding Hands: Scully holds Mulder's hand after he reads his sister's diary.
- I See Dead People: Mulder, as well as the parents of one of the victims.
- Monochrome Apparition: The children, including Samantha, are seen by Mulder with a pale blue tint to them.
- Myth Arc: The second part of a two-parter revolving around Mulder trying to find out what happened to a bunch of kidnapped children and ultimately, attempt to find his sister, alive or dead.
- Secret Diary: Samantha had one while she was kept at the base, detailing the tests done on her before she died. Mulder finds it hidden in the wall of the house.
- Villains Never Lie: Mulder and Scully go back and forth on this, the former intensely sceptical of the Cigarette-Smoking Man's story about Samantha, and Scully more or less willing to take him at his word, because he has no apparent reason to lie. For his own part, CSM claims that with the Syndicate destroyed, there is no longer any reason to protect their secrets. Turns out he was telling the truth. Samantha died.