pywren:

A Tale of Long Suffering by one Leonard H. McCoy

During the Five Year Mission Bones had to put up with a lot of shit. But
I’m pretty sure the mutual pining that permeated the air whenever his captain
and his favourite frenemy were even in the same quadrant of the galaxy is among
his personal top three.

Witnessing Jim’s desperation when Spock is in danger is something that
happens actually quite frequently, all things considered. And it probably cost
Bones a few years of his life whenever the Vulcan considered himself expandable
and put himself in harm’s way. But it was to be expected. Jim always liked Spock, however one wishes to interpret this, the “affection” was definitely there. 

BUT to witness Spock going bat-shit crazy when Jim is in peril is something
else altogether. Bones probably enjoyed it the first time it happened, just to
see Spock showing an emotion at all. And this, too, happened more than once over the course of the mission.

So yeah, Bones was DEFINITELY in the known on this one! While his best friends were still pining for each other from afar. HE KNEW. And he had to listen to them for the the entirety of the mission. (And the second mission, too, if we count TAS here.) 

But there is one thing that always puzzles me. It’s the well known scene from “Requiem for Methuselah”. 

MCCOY: Well, I guess that’s all. I can tell Jim later or you can. Considering his opponent’s longevity, truly an eternal triangle. You wouldn’t understand that, would you, Spock? You see, I feel sorrier for you than I do for him because you’ll never know the things that love can drive a man to. The ecstasies, the miseries, the broken rules, the desperate chances, the glorious failures, the glorious victories. All of these things you’ll never know simply because the word love isn’t written into your book. Goodnight, Spock.
SPOCK: Goodnight, Doctor.
MCCOY: I do wish he could forget her.
(McCoy leaves. Spock goes over to Kirk and initiates a mind meld)
SPOCK: Forget.

Sometimes I am almost convinced that Bones was trying to needle Spock into admitting something, ANYTHING at this point. Maybe because the mission was almost ending and no one knew where they would be stationed next. Or maybe because Jim’s loneliness drove him slowly but surely mad. I don’t know. I have no explanation for this scene other than calling it “the one scene where McCoy’s observation skills failed him”. 

I also keep thinking about the permanent raincloud over his head during the
Motion Picture Movie. He seems really pissed at the beginning. And I don’t think it’s because Jim “drafted”
him just as he sat down with a mint julep on his porch in Georgia or beamed him right out of his work on Fabrini medicine. 

I think it’s at least partly because
he had a front row seat for the big “whatever-happened-between-Jim-and-Spock”
at the end of the five year mission. He had to watch everything fall apart. No matter what he tried, the crew still drifted apart without their center. And he didn’t forgive Spock for running
away to Vulcan. And he certainly didn’t forgive Jim for just accepting the promotion
and letting Spock go.

One of the BEST PARTS of the TMP Novel may just be the bit where we, the audience, witness
the confrontation scene (the one before the Sickbay Scene^TM) between
Kirk and Spock from Bones’ point of view. He watches Jim despair over Spock’s
apparent lack of emotion. And his not-so-lowkey frustration about this entire situation shows it’s ugly head in the most entertaining way possible: biting sarcasm. (It’s peppered throughout the book, and a few scenes are shown in the movie as well.)

And the neat little tidbits of information we get by courtesy of Bones’ medical knowledge are fucking priceless! Because even IF Roddenberry didn’t tell us how
madly in love those two idiots were, you can bet your last cookie that Leonard
McCoy had to suffer through it all and he will shout it from the rooftops.