In the intro to this episode, when the tube is pulled from Mulder's mouth, it appears the same as the one pulled from Scully in the The X Files movie.
When Doggett picks up the file on Gibson Praise you can see that part of the number that is shown when he looks at it is 1013 which is Chris Carter's birthday.
When Scully points out the location of the last time they saw Gibson Praise, she points to the (real) Palo Verde Nuclear Plant, which is west of Phoenix. In 'The Beginning' the plant shown was the (fictional) Rolling Hills Nuclear Plant, 60 miles east of Phoenix.
Scully: John Doggett... You may as well have introduced yourself.
Doggett: Well, I was gettin' around to it.
(Scully looks at him for a moment, and throws a cup of water in his face.)
Doggett: How far would Mulder go?
Scully: How far would he go for what?
Doggett: The truth. His truth. Whatever it was he was trying to prove... How bad did he need to prove it?
Scully: It was his whole life.
The name of Mulder's mother is given in most X-Files sources as Teena; however, when the Mulder family tombstone is shown in this episode, her name is spelled Tena.
The Oxford Dictionary of English Names gives Tina as "...a pet form derived from names like Christina and Clementina, now used as an independent name." Hence, the usual spelling with an i; Teena is a much more recent form.
This episode marks the first major change to the opening credits since the show first started with new images, updated photos for David Duchovny and Gillian Anderson and the addition of Robert Patrick to the main cast.
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.
Agent John Doggett is named after sports commentator Vin Scully's co-commentator, Jerry Doggett. Vin Scully is the man after whom Dana Scully is named.
Dedication: In Memoriam - Jim Engh 1961-2000. Jim Engh was a member of the production crew who was electrocuted while filming a scene from a scaffold for this episode. Six other crew members were injured in the accident.
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