It wasn't really anything that was worth noticing, but Kirk noticed anyways. The only word Jim could think of to describe it was distance, Spock was putting a distance between himself and everyone else, more specifically Jim. But we tend to take things personally, and Kirk was doing his best not to.
It wasn't as if Spock wasn't declining to go to dinner, meeting Kirk for breakfast, and chess, walking with him to the bridge, no, he was there, punctual and polite as usual, but something was gone, something had faltered. If he looked at Spock for long enough while they were on shift, he would see it: tiny moments of pause, an exhausted pose, what seemed like an inability to work for only a minute fraction of time.
It took Kirk a great deal of thought, how does one approach an unnoticeable, perhaps invisible problem? But finally, with apprehension swirling chaotically in his stomach, he rang the buzzer to Spock's quarters; a little late in the evening for propriety, perhaps, but Kirk knew his friend would overlook that.
"Good evening captain"
" I think I'm Jim tonight, Spock"
"Jim"
Spock did not look as if he minded the disturbance, nor did his tone sound so, but there was something there, something slightly forced, a little bit of overcompensation. Kirk knew he couldn't just jump in, confront his first officer of a problem that had no evidence, so he walked into the room, sat at the desk, while Spock took the other seat.
"Can I get you anything?"
"No, no, Spock, how long ago where we on Organia?"
It had been a moment of insight, Kirk's memory suddenly flashing him the picture of Spock returning with the Klingons, saying "But it was an interesting experience", pale, gaunt, a little bit of humor to make everything as okay as possible so that Kirk wouldn't see something. But to the present, Kirk returned to a nine o clock evening with his first officer sitting across from him, stiff in the shoulders and wary.
"Two weeks, three days, and seven hours captain."
"Ah. And what was that mind sifter like?"
"You have my report"
"But for you?"
He watched Spock contemplate his answer, watched the light from the console dart across his face, watched and saw, once again, that slight fracture in the façade. For a moment he looked like a child. He had been right. Kirk closed his eyes, guilt washing over him. His first officer had been raped, worse than physically, his mind.
"Spock" he whispered, "It's okay, you don't need to tell me, I should have known earlier.
Spock looked up, and looked lost, and then remembered where he was, his low eyes pleading with Jim, his face paling, and Kirk found himself at a loss as far as what he should do, his face moved closer to Spock's, forced the Vulcan to meet his eyes, and nearly recoiled from the effect the torture in them had on him.
Spock closed his eyes, "I ask forgiveness"
"No", Jim said, "you have done nothing wrong, this wasn't your fault, none of this is, you didn't ask for it"
Spock's eyes remained closed, but his head now rested between the two fingers on each temple. Jim pushed his chair back,
"Come on, I'll make you some tea, go lie down, you haven't been sleeping well, I can see that"
He put his arm around the willowy shoulders of his first officer when he sat down on the bed, and was surprised at the relaxation, instead of tensing of the muscles he felt under him. Spock took a sip of his tea, swallowed, winced, and spoke, softly.
"The back up section of the mind sifter is, that, if it does not work immediately, it installs nightmares into the victims mind that last for several months, for a spy, who would be captive for that amount of time, it is a most successful way of, as they say, breaking them. They kill you in my sleep every night, and then set me free. I watch you die, Jim, every night, and every morning believe you to be dead, until you appear, magically before my eyes. My day is spent knowing you will be killed when the evening comes. It is most difficult"
Jim had nothing to say, there was little he could do. He took the glass from Spock's hand, and set it down on the bedside table, and brought the Vulcan closer to him, covering them both with a blanket, sliding down so they were comfortable to sleep.
'Get some rest my friend, I promise, I'm alive, and will be in the morning"