- After Action Patch Up: Scully treats Mulder's broken finger when he comes to his apartment.
- Continuity Nod: Mulder's anti-government rant at the UFO convention in "Patient X" appears to be what brought him to the group's attention as a possible defector.
- If I Do Not Return:Mulder: If you don't hear from me by midnight ... feed my fish.
- If You're So Evil, Eat This Kitten: Mulder's loyalty is tested when he is ordered to kill a wounded hostage. Turns out the group leader was a mole all along; that's why he suffered no repercussions
- Fingore: Mulder gets tortured and his finger gets broken.
- Right-Wing Militia Fanatic: The New Spartans, played monstrously straight.
- Something Completely Different: An X-Files episode without an X-File. No alien invasions, Myth Arc tie-ins, or Monster of the Week. Instead, it's a paranoid thriller about a group of terrorists with a genetically-engineered bioweapon.
- However, it still managed to be about government conspiracies.