Mulder learns the truth about the Syndicate that's collaborating with the alien colonists, just in time for the Syndicate to be wiped out by the alien rebels.
- The Bus Came Back: Marita Covarubbias, who has been infected with the Black Oil to test the vaccine. It seems to be working though she looks sick.
- Continuity Nod: Fort Marlene and it housing an alien fetus were previously established way back in "The Erlenmeyer Flask".
- Cryptically Unhelpful Answer: Mulder's "explanation" of events at the end. Not even Scully adds any facts to the conversation.Mulder: They burned themselves. With a choice made long ago by a conspiracy of men who thought they could sleep with the enemy. Only to awaken another enemy.
Kersh: What the hell does that mean?
Mulder: It means the future is here, and all bets are off.
Kersh: Agent Scully, make some sense.
Scully: Sir, I wouldn't bet against him.
- Deadpan Snarker: Mulder has a couple.Mulder: (while being checked for contaminants after the Decontamination Chamber) There must be some kind of mistake. I signed up for the aroma therapy treatment.
Mulder: (as Scully scoffs at a plain outfit after their clothes are burnt) I heard gray is the new black.
Mulder: Interesting company you keep.Cigarette-Smoking Man: No more interesting than your apparent lingerie fetish.
- CSM has his moments too.
- 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.
- Despair Event Horizon: Mulder has a subtle but notable one after his conversation with the CSM; he very nearly agrees to cut his losses and escape with the Syndicate.
- Decontamination Chamber / Shower Scene: Both Mulder and Scully get one in the same room, with just a little wall dividing them.
- Dropped a Bridge on Him: After being a constant looming presence in the background, the entire Syndicate (minus, naturally, the Big Bad himself) is Killed Off for Real.
- Disappointed in You: The Cigarette Smoking Man tells Jeffrey Spender as much before he kills him.
- Eating the Eye Candy: Both ways with Mulder and Scully in the Shower Scene.
- HeelFace Turn: Jeffrey Spender gives up the X-Files and recommends Kersh to reinstate Scully and Mulder.
- Hoist by Their Own Petard: The Syndicate's choice to ally with the alien colonists comes home to roost, and they die for it. Lampshaded by Mulder.Mulder: They burned themselves. With a choice made long ago by a conspiracy of men who thought they could sleep with the enemy. Only to awaken another enemy.
- Kill 'Em All: The Syndicate elders, along with their families, are killed by the alien rebels.
- Killed Off for Real: Cassandra Spender, the whole Syndicate and their families except CSM (and, it eventually turns out, Jeffrey Spender).
- Myth Arc: The episode wraps up a sizable part of the storyline—something that promotional material ran wild with.
- Offing the Offspring: The Cigarette Smoking Man kills his son, Jeffrey Spender, for his betrayal.
- The Quisling: The Syndicate members are revealed to be collaborating with aliens to protect them and their families from colonization by making an alien-human hybrid. They are actually buying time to make a vaccine but to their horror, succeed by making the first hybrid in Cassandra Spender.
- Redemption Equals Death: Jeffrey Spender's HeelFace Turn gets him killed.
- Screw This, I'm Outta Here!: CSM and Fowley once things start to go to hell.
- Shirtless Scene: Mulder in the Shower Scene.
- Sole Survivor: The Cigarette-Smoking Man is the only senior Syndicate member to leave this episode alive.
- Villain Has a Point: Mulder rails against CSM's actions on a moral level, but has a somewhat harder time refuting his rationale.