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Humans, Spock has come to learn, are secretive. Jim Kirk is no exception; in fact, where most humans only maintain a few closely-held secrets, Jim has made the practice an art form. It would not bother Spock—asking a human to cease being illogical is to ask gravity to cease functioning—but some of Jim's secrets are harmful.
It... there is no other word for it... it hurts Spock that Jim feels he cannot share certain things, however much he may know Spock is willing to listen, and to attempt to rectify the situation whenever possible. But accepting Jim is accepting Jim's well-hidden neuroses, and so when Jim does something that tells Spock that his secrets—secrets Spock is not privy to—are harming him, Spock must simply watch, and wait, and assist when it is possible, when it is allowed.
"Bones!" Jim snaps, in the middle of the officers' mess. Several lieutenants turn their heads at the sound.
"Jesus Christ, Jim, what?"
"Clean your fucking plate! Wasting food is a crime, especially on a starship!"
Dr. McCoy looks at the remains of his dinner. "Jim," he starts, but Jim's body is a tense line in his seat, vibrating aggression that Spock can feel coming from him in waves. McCoy sighs, mutters something Jim cannot hear but Spock can, about the efficient carbon usage of replicators, and sits down to scrape up the last of his food before depositing his cleaned dishes in the recycler. He casts a wary look at Jim and a quelling one at Spock before he leaves the mess; the noise level has resumed in the meantime. It is not the first time this has happened, after all.
"You show great diligence in your efforts to conserve food resources," Spock says, nearly offhandedly.
Jim starts, then slouches in his seat, digging his fork into his potatoes. "Mom was big on it, I guess it rubbed off," he mumbles.
Spock's mother was also steadfast in ensuring Spock finished his meals as a child, but Spock has not grown up to experience anxiety at the sight of wasted food, or to eat his meals at the speed of one who expects it to be taken away from him. But Spock does not say anything, and merely accepts the lie.
Jim is a complex creature, shaped by his experiences, and Spock loves his complexities, would not have him otherwise. Dr. McCoy warned him once, years ago, that Jim has 'emotional baggage', unknowable and crippling, and that he would not blame Spock to stay away but that Spock would also not be the one to 'fix him'. The implication of that statement was that if Jim had some problem to be diagnosed and fixed, McCoy would long since have done so. Spock could not fault his logic as a medical practitioner (however suspect in ability from time to time), but also did not appreciate the implication that he did not think Jim adequate in his current psychological state. A fallacy, as he had already fallen in love with Jim by then and could never find him inadequate.
And so Spock copes with Jim's idiosyncrasies, appreciates his infectious humour and insatiable sex drive, and endures the nightmares that overtake Jim from time to time, occasionally leading to sleepwalking. Spock lies with him and holds him when he can, and listens to the screams and the warnings and the sobs, and tries not to scream and sob with him, because Jim keeps his anguish a secret when he is awake, but asleep, he cries for his aunt and his childhood friends, yells obscenities at Governor Kodos.
Jim volunteers the Enterprise to intervene in genocides while refusing to explain his reasons to anyone, including Admiral Pike, including Dr. McCoy, including Spock. He has sleepwalking episodes after each of those missions and spends several days afterward jumping at shadows and being extremely affectionate with Spock. Any time he experiences shock, this happens without fail. But eventually, his smile comes easy again; he eats marginally slower and sleeps better, and Spock allows him his secrets.
