- Continuity Nod: Fort Marlene and it housing an alien fetus were previously established way back in "The Erlenmeyer Flask".
- Death by Irony: The Syndicate had previously decided that siding with the alien rebels would be suicide. Not doing so is what gets them killed.
- Go Out with a Smile: Cassandra Spender.
- Heel–Face Turn: Jeffrey Spender gives up the X-Files and recommends Kersh to reinstate Scully and Mulder. Gets him killed for his troubles.
- Killed Off for Real: Cassandra Spender, the whole Syndicate and their families except CSM.
- Eventually subverted with Jeffrey Spender.
- Myth Arc: The episode wraps up a sizable part of the storyline—something that promotional material ran wild with.
- Screw This, I'm Outta Here!: CSM and Fowley once things start to go to hell.