David Duchovny finally settled his long-running legal dispute with Fox over the syndication of the series just three days before the episode aired. Once that concluded, discussions could take place about the future of the show. Duchovny had already expressed his desire to step away from the series but was persuaded to sign on for Season 8 in a reduced role.
There were so many special effects required for this episode that 5 FX houses were outsourced to work on it, most of them having to do 24 hour shifts to get it all done. The special effects were all completed the day before this episode aired.
Kim Manners' first cut of the episode ran 12 minutes over the requisite 42 minute running time. He had 2 days to whittle that down into shape.
Chris Carter originally planned to write and direct what he assumed would be his farewell to the series. But as the story took shape, he felt that Kim Manners would have a better handle on the material.
The only time Krycek and Covarrubias personally interact with the Lone Gunmen. The only other time Skinner interacts with them after En Ami (2000).