Buried Alive: Krycek ends up locked in a top secret silo several storeys under the ground. The trope is also used thematically, as Scully recalls what she was told in the prior episode about the dead always speaking to the living.
Genre Savvy: The Well-Manicured Man is certain the man who shot Skinner is one of CSM's underlings. He also advises CSM to clean up the mess before Skinner can ID the shooter, as nothing then would be able to stop an arrest.
Mulder puts the pieces together to ascertain what really happened to the submarine crew.