Executive Meddling: The original outline was approved by NBC program manager Stan Robertson, with the conditions that "the highly cerebral portions of the story would be eliminated and the complex nature of the plot would be materially simplified".
What Could Have Been: The original draft had Sargon and Thalassa continue their existence as spirits without bodies, floating around the universe. However, atheist Gene Roddenberry, who did an uncredited re-write on the script, changed the ending to the aliens fading out into oblivion. This led to devout Catholic John T. Dugan using his pen name John Kingsbridge in the episode's credits. When he said "into eternity", he meant "into eternity," darn it:
That line totally went against my philosophy and cosmology. I didn't want to be associated with it. This oblivion idea is Roddenberry's philosophy, not mine. My philosophy was that these entities would exist as spirits for eternity, but they wouldn't have their bodies. That might be a small thing, but I have a reputation and a philosophy, and everybody who knows me knows what I stand for; I certainly dont stand for oblivion in the afterlife. So I used my pseudonym. When you write a script, you don't expect to have your "world view" changed by a producer. The rest of Roddenberry's changes were all trivial, as I said in my letter to the arbiters; the big thing was the change in the episode's philosophy." - Dugan, quoted in These Are The Voyages, TOS Season Two.