Followed by one of the only three explicit references to using the toilet in all of Star Trek. 
edit: for those wondering, the other two are:
VOY - S05E12 - ”Bride of Chaotica!”
Neelix: Replicators aren’t the only systems of convenience offline. We’ve only got four functioning lavatories for a ship of a hundred and fifty people.
ENT - S01E08 - ”Breaking the Ice”
When Miss Malvin’s fourth grade class from Worley Elementary School in County Kerry, Ireland sent letters to Enterprise NX-01 later that year, Molly McCook wanted to know “When you flush the toilet, where does it go?” After Captain Archer passed the question to Commander Tucker, he responded with: “A poop question, sir‽”
Technically, there are some rather oblique references made to “waste extraction” by Rom and other Ferengi in DS9, which I’m not counting here, as they are neither explicit references and also raise some terrifying questions about the Ferengi process of using the toilet.
edit 2: in each of these 3 examples (including FC), each is the only time the words “pee”, “poop”, and “lavatory” and the phrase “take a leak” are ever mentioned in all of alpha-canon Trek.
as an interesting aside, one other phrase used to be extremely rare in Trek, only appearing about 3 times pre-nuTrek:
“Oh, my God”, “My God”, or any utterance of the word “God” as an exclamation.
Once, during the transported accident in Act I of TMP, uttered by Kirk because what happed was just that shocking, and another couple of times, I believe in DS9 and VOY. The reasoning behind this was because Roddenberry believed that everyone in the future were atheists because humanity had long past evolved beyond the concepts of superstition, the belief in the supernatural, and religion, so this sort of exhortation of shock or disbelief was so antiquated, it had fallen out of common parlance long ago.
However…, since nuTrek has made everyone in the future filthy potty-mouths, this particular phrase (and its variants) abound. Not that lazy, slapdash nuTrek dialogue is especially sparkling in any other respect, but this one rule being cast aside really annoys me because Roddenberry’s reasoning for why it fell out of use makes sense. I understand that people in the future would still use explicit language - and that the word “fuck” is immortal - but that sayings like, “Oh, my God!" would disappear after 2-3 centuries of almost everyone everywhere being atheists.
there’s another stray reference in VOY by a Bolian crew member to “waste extraction” I didn’t include, and, iirc, another in DS9. from lines dropped throughout Bermaga-era Trek, they are intimated to be prolific poopers.
There is the one TOS alternative Earth episode where it ends with the presumption that the rebellion was sparked by a Sun-worshiping religious movement, and Uhura corrects the others by saying it wasn’t the Sun, but the Son of God. But your point is correct that for the most part ST has always been atheist/humanist leaning and that is why that ending felt out of place.
ya know, TOS actually has a handful of crypto-christian references in it here and there. nothing really explicit, however, this one example is about as on-the-nose as it gets. It never touches on it like that again.
I remember seeing this a thinking, “WTF‽”
1960’s TV wasn’t ready for a spaceship full of atheists. A Russian and a black lady on the bridge was already pushing the boundaries of tolerance well past what lots of people could handle. Tell the audience that the entire galaxy is, like, over God… yeah, you’re going to get NBC affiliate stations fire-bombed. Shit, that happened to a station in Tennessee when Kirk kissed Uhura….
Yes, it’s absolutely because of the audience of the time, and possibly the writer(s). Maybe they snuck the ending shot in before anyone could realize and it was either spend more money and time to redo or just go with it. That’s exactly how Shatner got the kiss into that other episode, by ruining the rest of the “more accepted” takes.
It’s also why the 80s and 90s movies and shows still have references that we can relate to. A true 23rd/24th century script would not do well even if shown now.
“Here?”
“Uh, actually, over there”
Followed by one of the only three explicit references to using the toilet in all of Star Trek. 
edit: for those wondering, the other two are:
Technically, there are some rather oblique references made to “waste extraction” by Rom and other Ferengi in DS9, which I’m not counting here, as they are neither explicit references and also raise some terrifying questions about the Ferengi process of using the toilet.
edit 2: in each of these 3 examples (including FC), each is the only time the words “pee”, “poop”, and “lavatory” and the phrase “take a leak” are ever mentioned in all of alpha-canon Trek.
as an interesting aside, one other phrase used to be extremely rare in Trek, only appearing about 3 times pre-nuTrek:
“Oh, my God”, “My God”, or any utterance of the word “God” as an exclamation.
Once, during the transported accident in Act I of TMP, uttered by Kirk because what happed was just that shocking, and another couple of times, I believe in DS9 and VOY. The reasoning behind this was because Roddenberry believed that everyone in the future were atheists because humanity had long past evolved beyond the concepts of superstition, the belief in the supernatural, and religion, so this sort of exhortation of shock or disbelief was so antiquated, it had fallen out of common parlance long ago.
However…, since nuTrek has made everyone in the future filthy potty-mouths, this particular phrase (and its variants) abound. Not that lazy, slapdash nuTrek dialogue is especially sparkling in any other respect, but this one rule being cast aside really annoys me because Roddenberry’s reasoning for why it fell out of use makes sense. I understand that people in the future would still use explicit language - and that the word “fuck” is immortal - but that sayings like, “Oh, my God!" would disappear after 2-3 centuries of almost everyone everywhere being atheists.
And this is why we need Tom Hanks in a Trek cameo, even if under heavy prosthetics.
Neelex: “…especially the Bolians”
That line has had me curious for some time. They’re just blowing up any/all restrooms they encounter?
there’s another stray reference in VOY by a Bolian crew member to “waste extraction” I didn’t include, and, iirc, another in DS9. from lines dropped throughout Bermaga-era Trek, they are intimated to be prolific poopers.
There is the one TOS alternative Earth episode where it ends with the presumption that the rebellion was sparked by a Sun-worshiping religious movement, and Uhura corrects the others by saying it wasn’t the Sun, but the Son of God. But your point is correct that for the most part ST has always been atheist/humanist leaning and that is why that ending felt out of place.
ya know, TOS actually has a handful of crypto-christian references in it here and there. nothing really explicit, however, this one example is about as on-the-nose as it gets. It never touches on it like that again.
I remember seeing this a thinking, “WTF‽”
1960’s TV wasn’t ready for a spaceship full of atheists. A Russian and a black lady on the bridge was already pushing the boundaries of tolerance well past what lots of people could handle. Tell the audience that the entire galaxy is, like, over God… yeah, you’re going to get NBC affiliate stations fire-bombed. Shit, that happened to a station in Tennessee when Kirk kissed Uhura….
Yes, it’s absolutely because of the audience of the time, and possibly the writer(s). Maybe they snuck the ending shot in before anyone could realize and it was either spend more money and time to redo or just go with it. That’s exactly how Shatner got the kiss into that other episode, by ruining the rest of the “more accepted” takes.
It’s also why the 80s and 90s movies and shows still have references that we can relate to. A true 23rd/24th century script would not do well even if shown now.