This episode - a Walter Skinner-centric one - sprang from David Duchovny's request that he and Gillian Anderson play a lesser role in order to have some time off. Being the 21st episode in the season, most of the cast and crew were exhausted at this stage.
Mitch Pileggi's sex scene with guest actress Amanda Tapping was supposed to be a closed set, but David Duchovny insisted on barging onto the set and giving him notes.
This is effectively the first time in the series that the episode is centered on someone other than Mulder and Scully.
In Sanskrit, "avatar" means the incarnation of a deity.
According to the certificate in the box in Skinner's living room, his middle name is Sergei.