 This episode was written by Glen Morgan and James Wong and directed by David Nutter . Originally , the season two premiere was supposed to be written by series creator Chris Carter . In the rough draft of this version , Mulder would have been sent to Moscow . Carter , instead , assigned Morgan and Wong the task of writing the season opener . Before working on The X @-@ Files , Morgan had written a script with the same name about a man who goes to a telescope located in Chile . The script was never made , but Morgan liked various elements of it , so he cannibalized parts for " Little Green Men " . In addition , the episode was specifically written for Mulder to question himself and his beliefs . According to the two writers , one of the main themes of the episode is “ the idea that we all have to fight our own little green men and carry on . ” 
