He has noticed the captain's aversion, though he continues to be ignorant of the cause. For all that he nearly strangled the man to death on the bridge, Jim shows no hesitation when Spock touches his neck. He has even placed Spock's hands there himself in the heat of passion, something which Spock admits to himself that he does not understand.
But he can think of no reason for Jim to deny him contact with his face, his mind. So he concludes that logically, since it is James Kirk, he must be doing it as a tease, trying to see how far he can push Spock before he pushes back. The theory is in accordance with the captain's nature, and Spock is content with his conclusion.
Until the night he finally chooses to push back, intentionally maneuvering them so that Jim is underneath him, so that it is almost impossible for him to avoid Spock's fingers.
The instant that he brushes against Jim's mind he knows that he's made a mistake. The arousal is gone as if it had never been, Jim's mind an unthinking whirlwind of terror and desperation and remembered pain.
Spock doesn't even feel the blow that nearly breaks his nose, all his attention focused on blocking the torrent of emotion that is still streaming from Jim's panicked mind. When he finally has control over himself he looks for Jim, and his heart nearly breaks when he sees Jim hunched in on himself in the corner like a child.
And he feels an all too human surge of shame, that his actions have done this to his captain. His friend. That he did it in ignorance is no excuse.
Eventually he slides off the bed, not bothering to reclothe himself, and moves so very slowly towards Jim. The man is already nearly hyper ventilating, and the last thing Spock wants is to frighten him further. When he is finally next to Jim he kneels, making certain to keep his hands in sight and far from Jim's pale face.
"I apologize for my presumption, Jim. I was unaware that you would find my mental presence so...distasteful." What he means is traumatizing, but he can't quite make himself say the word.
Jim closes his eyes for a moment, obviously trying to pull himself together. "Not your fault, Spock. You didn't know. No way you could have."
Spock tries to ignore the way Jim's voice shakes and focus on the words themselves. "What couldn't I know, Jim?"
The blue eyes are open now, red rimmed and slightly wet, but meeting his own. "He did it, on Delta Vega. It was the only way to show me what I needed to know. It hurt."
At Jim's hesitant admission, Spock feels his blood run cold. It may have been necessary, but the older version of himself had done the unthinkable. He had purposefully violated the mind of a man he had dared to call friend.
He dares to rest one hand against Jim's bare knee, and is relieved when he doesn't flinch. "Jim, it should not have been that way. Done properly, and with knowing consent, there is no pain. If I had known what he did, I would never have attempted it without first explaining things to you."
Jim is silent for a long moment, and Spock is content to simply kneel there with the only point of contact between them his hand on Jim's knee. Whatever it is that Jim needs, Spock fully intends to see that he gets. Eventually, though, Jim speaks.
"It really shouldn't hurt?"
Spock shakes his head. "No. It is meant to be a comfort, a way to connect more fully with family, or a partner. I believe that my counterpart on some subconscious level mistook you for his Jim Kirk, and so did not think to explain anything to you before he acted."
Jim bites his lower lip, then takes a deep breath. "Okay. Try it again, but nice and slow."
He blinks, not entirely certain that he heard Jim properly. "You wish me to attempt a meld again, now?"
Jim nods. "Yeah, I do. I trust you, and if you say it'll be different then I believe you."
Spock has no idea what to say to a display of trust like that, so he says nothing. Instead, he slowly extends his free hand towards Jim's face. If this is what his friend thinks he needs, then this is what Spock will give him.
Jim flinches slightly as Spock's fingers touch his face, but when Spock carefully and gently brushes against the bare edges of his mind Jim's eyelids flutter and his entire body relaxes.
There is no pain this time. No grief and no guilt burning like Vulcan's former sun. This time, Spock knows Jim is feeling only pleasure, warm and soft and bright. There will be time for sharper pleasures later, for heat and arousal and lust. For now, he simply wraps Jim in a mental embrace and lets him float.