The day Spock noticed the clouds.
He hated Jim. It was more likely than the third option but it still made him incredibly uncomfortable. Vulcans are not meant to hate but he was only half Vulcan. Jim treated him as a friend with trust and affection, and he may hate him. There were a few reasons, that he could think of that some people may (perhaps him included) see as reasons to hate their captain. There was that day, the day that he felt happy, the day Jim took it away from him.
He had never noticed the clouds never felt this rush of.. of? He had never felt it so he couldn't quite identify it but from what he had read it was perhaps elation, or maybe the elation was due to something else. Contentment, happiness, maybe these things. Then there were the feelings not there, the feeling of not fitting was gone. He belonged, he belonged here, he belonged with Naomi. He liked these feelings, and these sensations, the slightly musky scent of his coupling with the soft tender woman beside him. The sound of her slow breathing and feeling of her skin against his, cool compared to his. He felt another new sensation, a kind of tightness in the region of his heart A whirlwind sensation in his stomach region. He had named this love, he had told her without reservation that he felt love for her. He wanted to spend endless days here, working in the morning on the farm and then making love under the warm sun of the mid afternoon, sleepy evenings curled together reading books and falling asleep next to each other. It was a pleasant thought, one he had never considered to be a valid option for his life before.
Naomi had been pointing at clouds and translating their random shapes into those of familiar objects. He listened to her fascinated by the child like game then noticed one cloud that did actually remind him of a dragon, how a cloud could look like a dragon he did not know.
" That one looks like a dragon." He said pointing up at the sky.
" I have never seen a dragon before."
" I have on Alfa seti five. But I have never stopped to look at the clouds before."
He started wondering about clouds and rainbows and how delightful they were and how it was he had never noticed before how delightful they were then the dizzying happiness flooded him again and he turned to Naomi and found those soft lips waiting for him.
Jim had taken the happiness away, replaced it with anger, anger at his friend calling his mother an encyclopedia, his father a computer, telling him he was an over grown jack rabbit and saying the words he had secretly always feared that he was not worthy of love, not worthy of loving anybody. It was illogical but it was something his human side seemed to cry out for.
He knew of course that the happiness was an unnatural one and that he would have wasted his life in farming and making love without a care for scientific inquiry. It was wrong, he had been born with the mind of a scientist, he received, if not happiness then at least fulfillment from answering the questions of the universe, discovering the before undiscovered. He knew that it was illogical to miss something he had barely glimpsed and to feel some resentment at it's loss but he briefly had done at the time. When he had held Naomi for the final time and told her the truth that he was not built for joy, that he had chosen to dedicate his life to star fleet, to serve the crew and his captain the man who as he spoke those words he felt some illogical anger towards.
Did he still hate Jim? Did he unknowingly still feel that resentment? Was his Human side more in control than he thought it was? Certainly in those rare times when he had become tired and forgone meditation he had found himself thinking of the day he had looked at the clouds and felt happiness and had felt a strange half longing for some element of it, the warmth of another body besides his own. The relaxed hazed after love making and the relaxed company whilst laying on the grass resting. But he did not miss Naomi herself, in fact when he thought of these things another face came into his mind.
He did not wish to hate Jim. But he could understand why his Human side might. It was not just that he had taken away the only semblance of happiness Spock had ever felt, there were other reasons as well.