Gillian Anderson, who appeared in more episodes of The X-Files than all other cast members, took one week off from the series to film her role in The Mighty (1998). The writers decided to create another story centered around Skinner and his involvement in the deal made with the cigarette smoking man to cure Scully's cancer, as alluded to in Memento Mori (1997).
There is a dedication: "In Loving Memory of Vito J. Pileggi," father of Mitch Pileggi. Vito died in the same month the first X-Files episode Pilot (1993) aired.
One of the folders in Mulder's files at the 23:30 mark was "Foo Fighters." Many people will think of the band Foo Fighters, but the group actually got its name from the UFOs and various aerial phenomena that were reported by Allied aircraft pilots in World War II, which were known collectively as "foo fighters."
Visual effects supervisor Laurie Kallsen-George had only 9 days to create the bee attack sequence, something which would normally take months on a feature film.