When Doggett thanks the Lone Gunmen for coming, Byers says, "Yeah, like we've got anything better to do these days." This is an in-joke referring to the cancellation of the spin-off series The Lone Gunmen (2001).
This is the final appearance of Mulder's apartment.
Lucy Lawless took on the role of Shannon MacMahon partly because her daughter was a big fan of the show.
Initially, it wasn't clear if Chris Carter would be returning to the show as his contract had expired. Carter encouraged the crew to start developing ideas without him and he was extremely excited by the ideas generated that he signed for another season.