Rocky Bronzino, an entomologist, is shamelessly hitting on Scully. This is an internal joke about Bamby, the entomologist Mulder flirted with in War of the Coprophages (1996).
Aaron Paul guest stars in this episode. He is one of a number of X-Files guest stars who went on to star in X-Files writer/producer Vince Gilligan's series Breaking Bad (2008).
Natalie drives a Beetle, a visual pun on the theme of bugs.
Having done lots of heavy-duty serious episodes, Robert Patrick had some difficulty adjusting his acting style to fit with something more frivolous.
"Lord of the Flies" is an English translation for the name of the semitic demon Beelzebub.