Question: Why was Deep Throat killed?
Question: How was Tooms able to beat the lie detector test?
Answer: The polygraph machine only works on those with a perceptible change in body physiology while they lie. It really only measures what we consider nervous reactions associated with lying. Psychopaths and sociopaths such as Tooms are extremely difficult to measure with this machine since they do not feel remorse for their actions, and as such typically do not get nervous when lying.
Question: Does anyone know the actual events that this episode was based on?
Answer: The title screen on the pilot episode actually said "based on documented accounts" not "actual events" which is kind of true - there are many claims of alien abduction - so technically the caption isn't false, but the episode was entirely fictional and not based on any real occurence.
Question: When they're flying on the plane, Scully starts breathing deeply and looks like she's afraid of flying. Has this ever been explained later? In all the later episodes, they never say she was afraid of flying.
Answer: She's afraid in this scene because the plane has encountered turbulace and is diving down. No fear of flying has ever been mentioned.
Question: While following Tooms, Mulder specifically says that he can't find his Norwegian Elkhound named Heinrick, who he goes moose-hunting with. I know that he is lying about owning a dog, but why the odd details? Am I missing a joke?
Answer: Mulder is not supposed to be watching Tooms. He is making up details on the spur of the moment, so he can pretend that he has a legitimate reason for talking to a dog-catcher.
Answer: To show that no-one is safe from the men behind the conspiracy, no matter who they are.They'll do anything to protect themselves.