The  show begins, intense sci-fi music plays as the ‘space ship’ come onto  the screen, as the camera pans up to the man fixing the telephone poles.  Even the beginning scene of the X-Files season 3, episode 20, Jose  Chung’s ‘From Outer Space’, is full of perception creating reality. As  we see the ‘space ship’ enter the scene we already assume its a  spaceship because perception tells us so. After watching the whole  episode, although every character was very interesting, the Pilot,   Lieutenant Jack Schaefer caught my attention. He’s interconnected with every ones  stories, and he had me most convinced throughout the episode. It brought  me to think Mulder wanted to believe the pilot could explain what  happened so he perceived his story to be real to give himself some sense  of reality.
The  first time we see the pilot, although we don’t know its him yet, is  through the boy, Harold’s point of view. Harold is telling Mulder and  Skully about what happened the night of the abduction. He’s the grey  alien smoking on the ship, which later makes you think the boys story is  correct for seeing the pilot smoking. The boy says the gray alien “was  just talking...in English, he just kept saying the same thing over and  over again ‘this is not happening, this is not happening’”. By seeing  him from the boys perspective we get an idea that he was real, that he  actually was abducted along with the two kids. Later on the man, Roky  Crikenson gives Mulder and Skully his script form story of the events  that night. He says he saw the two grey aliens and one third alien. One  of the gray aliens was obviously the pilot, thus planting the pilot, or  one of the aliens, at the scene in which Mulder had read, putting the  pilot there in his mind. Finally Skully is dissecting the dead alien  body they had found. Upon the autopsy, she notices a zipper and they  then realize the gray aliens were men in suits, Military men. Its then  that Mulder finds out that the dead man was in the Air Force, planting  the idea that its the government in his head. He tricks the Military  into giving him the name of the other grey alien, and finds out  Lieutenant Jack Schaefer is the other gray alien. 
Now  we are hearing Mulder’s story from Skully’s point of view. She says  ‘his account of things get a little odd’, so we aren’t sure if any of  the following actually happened, it’s just what Mulder said happened.  While he’s driving he runs into the Jack Schaefer walking naked down a  dark road. He’s scratched up and looks dazed. Mulder calls his name and  he grabs him repeating “this is not happening”. We hear him say this  again, once on the ship as the gray alien and again now. In Mulder’s  mind it’s what Schaefer would say, but we can’t be sure he was even  there. The scene goes onto Mulder talking to Schaefer in a dinner. Jack  Schaefer lights up a cigarette and tells Mulder many things, he tells  him he’s the pilot of a flying saucer. The government abducts people,  they take them “back to their base, let the doctors work on them nothing  physical they just mess with their minds”, Mulder replies “hypnosis”.  From this scene we know Mulder already knows the girl may have been  hypnotized and so thinks that's what the government would do try  experiments on. Everything in this scene is evidence Mulder is just  making the pilot up. He says things that have already been said,  solidifies facts that Mulder wasn’t sure was true, but wanted to  believe. The pilot goes on to say he’s “sure that him his co pilot and  those two kids were abducted”, but then says he can’t be sure of  anything, “I'm not sure were even having this conversation, i don’t know  if these mash potatoes are here...”. It seems like answers and the  whole scenario straight from Mulder’s mind. As the government storms in  to abduct Lieutenant Jack Schaefer. We then find out that the cook who  works at the dinner says that Mulder was there alone, asking him  questions and ordering pie with every question he asked. This seems more  like Mulder than when he was talking to the pilot. One more piece of  evidence to tell us Mulder thought the conversation with Jack Schaefer  was in his head, making all the loose ends he couldn’t figure out make  sense to him by the pilot telling him what he wanted to hear. 
Throughout  the episode the stories we hear about and the people Mulder and Skully  talk to all combine into the conversation with Milder and Lieutenant  Jack Schaefer. We get a sense of closure with this conversation. We get  the idea that Lord Kimboo is real, that the boy and girls stories match  up, that the government is behind all the abductions and that there are  really aliens out there. All of Mulder’s questions are answered too.  Every piece of pie Mulder ate was the reality, and the beat up pilot was  only the perception Mulder made for himself. 
