- Grand Inquisitor Scene: This episode features two lengthy ones, with the Cigarette-Smoking Man and Jeremiah Smith debating the merits of humanity and "the Project" in a prison cell. Closely modeled on the Trope Namer, The Brothers Karamazov.
- It May Help You on Your Quest: Mulder's mother directs Mulder to look for a device — a spike weapon — for killing green-blooded alien clones. Subverted because he never successfully uses on an alien.
- Myth Arc