- Deconstructed Trope: Turns out The Men in Black live mundane lives as well, and aren't any closer to the Truth than Mulder is.
- "Freaky Friday" Flip: Agent Mulder and an Area 51 security officer get mind-switched.
- Negative Space Wedgie: The tear in space generated by the spaceship's damaged cloaking device. Causes the "Freaky Friday" Flip and Telefrag effects. Fortunately, it has a built-in Reset Button in the form of Reverse Polarity.
- Ontological Inertia: Played with. If they can be in the right place when the snap-back happens, Morris and Mulder will get sorted out like the pilot and the old woman did, complete with a Reset Button resulting in it being "like the past few days never happened." The fused coins and the waterbed, however ...
- The Un-Reveal: When Mulder finally gets to speak with his confidential informant, the informant reveals... that he has no idea what the true nature of their work is. Nobody at Area 51 knows what the experimental aircraft are, they simply test them. He called Mulder in the hopes that Mulder could tell him if aliens actually exist.