Yes, it was The Omega Glory. Not anybody's favorite episode. Or close to it. It was, however, an episode written by someone with a lot of voice in deciding what episode should be used. It's also an episode with a very odd history. It was originally one of the three episodes written as a possible choice for the show's second pilot (along with Mudd's Women, and Where No Man Has Gone Before, the one they actually used). It was rejected as the pilot episode, largely because, (according to Joel Engel, in "Gene Roddenberry, The Myth and the Man Behind Star Trek"):

Roddenberry's The Omega Glory was clumsy. It concluded, after an improbable cat-and-mouse chase, with Spock getting fried by a laser beam, which allowed the captain to dispatch the villainous turncoat. "The Captain hurries to Spock whom we find lying on his face, his body glowing strangely," it read. But Spock's not dead, because "his home planet is a place of volcanoes and fire... lovely, lovely heat which sustains and heals but never destroys those who are born there."

Uh.... yeah. Well, thank goodness they didn't film that version. But there must have been some other problems with it, because while the other rejected pilot script, Mudd's Women was filmed almost immediately after the show went into production, Omega Glory never got made until the end of the second year. Some hints about this can be found in a 1967 memo from NBC exec Stanley Robertson to Producer John Meredyth Lucas:

On March 25, 1966, prior to the production of the first season of Star Trek films, agreement was reached in writing with Gene Roddenberry that the above titled script would be placed in "inventory" and at his discretion reworked and again submitted to us at a future date for our re-evaluation. Except for a few minor changes, we cannot distinguish enough difference in the 1966 script and the script received last Wednesday, November 28, to warrant an approval. Our basic objections, as discussed at great length with Mr. Roddenberry in 1966 are still, we feel, valid.

We will, however, on the basis of my telephone conversation with Gene Roddenberry on Monday morning in which he promised to "personally re-write Omega Glory to our satisfaction" prior to it's [sic] being produced, grant you an approval based on those conditions.

I must remind you again, John, that we, in the future will take an arbitrary position, regardless of production schedules, that no story for Star Trek will be approved unless you and your staff adhere to the clearly spelled out contractual requirements. -- Inside Star Trek, p. 197-198

Unfortunately, neither the book nor the memo tells us what these problems were. Presumably nothing to do with low quality, since those problems weren't fixed in the final product. Desilu Executive Herb Solow and Producer Bob Justman say this about it in Inside Star Trek:

HERB:   Gene Roddenberry's script, "The Omega Story," [the episode's original title] wasn't very good. It was unnecessary to point it out to him; he was the first to recognize the fact. It later became a less-than-mediocre series episode.

BOB:   Gene had mentioned several times that, when he was first submitting scripts to producers, he found one invaluable tool that helped guide his writing: Lajos Egri's The Art of Dramatic Writing.
          He kept the volume at his desk and said, "I use it all the time, Bob. If a writer follows its principles, he'll never go wrong. I think you really should have a copy."
          From the tone of his voice, I assumed he would spring for another copy or at least loan me his. I waited a week, but no such luck! So I went out and purchased one myself. Egri's writing style was dull, but I appreciated the principles he laid out, and I gained a better understanding of the elements of drama.
          Ironically, I later used Egri's principles to review Gene's own script, "The Omega Glory." I wrote a memo in which my comments were devastating. However, not wanting to hurt his feelings, I tore up the memo and made a few suggestions orally. He took the advice, but as anyone who has seen the episode knows, it didn't do much good.

Okay, so what's the point here? The Omega Glory sucks. We all know that, right? Right. But the point is, that however bad the televised version is, the Viewmaster version is even worse! We're talking true omigoshgolli Kiddie Trek. Well, in that case, why not sweep the whole thing under the rug (or KEEP it swept under the rug), and forget the whole thing ever existed? Well, a couple of reasons.

First because I personally saw the Viewmaster version before I ever saw the televised episode. As a result, I've never disliked this episode quite as much as I should have, simply because it's so much better (by comparison) than my first exposure to it. Secondly, because shows like Mystery Science Theater 3000 have brought an appreciation of cheesy movies into the mainstream, and there are bits of cheesy goodness in this Viewmaster version that should not be allowed to fall into obscurity. If you like creeping acronymization (what can one say about a crew that watches the action on their M.V.S., or Main Viewing Screen?), bizarre jargon (the Enterprise being referred to as "The Big E", something it was never called in the show), extreme overuse of quotation marks, and intense melodrama (Kirk screaming "Not if it means murder!" when Tracy tries to recruit him), well, the Viewmaster version has all these things and more. Spock's famous "F.S.N.P." alone is worth the price of admission.