The titles of this two part season premiere 'Within' and 'Without' is from a line by Deep Throat in the season 3 premiere 'The Blessing Way'. When Mulder talks to him in the dream state, Deep Throat says "Go back. Do not look into the abyss or let the abyss look into you. Awaken the sleep of reason and fight the monsters within and without."
Addition: And yet it seems odd they titled them this way round, since in the opening episode, the characters are 'without' Mulder, Scully is without someone she cares about so much, and Skinner and Scully must go without their belief in what happened to Mulder, as in not revealing it to anyone. In the second episode, they have an alien 'within', who could be anyone and there is much distrust of who it could be.