 The majority of the episode — like the rest of seasons six , seven , eight and nine — was filmed in and around the Los Angeles , California area . Before shooting the episode , Chris Carter reminded Patrick various times that he had to be in " good shape " . On the audio commentary , Patrick remembers being " nervous " for the shooting of the episode , since he was a big fan of The X @-@ Files before becoming a part of the acting crew . The scene in which Walter Skinner tells Doggett that he himself witnessed Mulder being taken away aboard a UFO was filmed in the second part of Patrick 's first night of production on the series ; this scene also marked the first time that Patrick got to work with Pileggi . The ending of the episode , as well as a majority of its follow @-@ up " Without " were filmed at Split Mountain in Anza @-@ Borrego State Park . According to producer Paul Rabwin , an " incredible heat wave " hit the area during the shooting , resulting in terrible filming conditions . In the desert , the cast and crew were informed that there was a " one in twenty @-@ five " chance that someone would be bit by a rattlesnake . Pileggi later joked that during the filming of his scenes all he could think about was stumbling upon a snake . 
