Spock kept a close eye on Dr. McCoy through the observation window, refusing to leave until he had proof that Khan's blood would be enough. Once the transfusion was complete, the doctor studied his medical scanner for a moment before turning to nod at Spock. There was a wide grin on the man's face that told Spock all he needed to know. The Captain would recover.
Spock returned the nod with one of his own and turned sharply on his heel to leave the hospital. He made his way across the Academy campus to the small apartment he kept for layovers on Earth. Now that he knew that his friend was alive, he needed to meditate in order to regain his own inner calm. His mind was in turmoil and he knew that he was unstable; dangerously so, if his encounter with Khan was any indication.
There had been no doubt that Khan had to be stopped, and the superior strength afforded to Spock by his Vulcan biology had made him the logical choice to do so. However, to say that his actions had been rooted in logic was more of a lie than the one that he'd told Khan about the torpedoes.
He was forced to admit to himself that he had been emotionally compromised by Kirk's sacrifice to such a degree that none of his actions had actually been undertaken logically. He had been filled with such fury that every move he had made was dictated by that inner fire. And worst of all, he had been so focused on ending the life in front of him, the one responsible for killing his friend, that he had nearly ruined any chance to save Kirk in the process.
When he reached his apartment, he prepared to meditate. Once he was settled on the floor, the soft tendrils of incense smoke luring his mind into a deeper calm, he began to analyze his actions and reactions over the past day, starting with the most disquieting—his tears.
Spock could not recall the last time he had cried. There had been a few times in his childhood that he had turned to his mother for comfort, his face damp, but they were hazy memories, and by the time he was old enough to begin his education he had long since buried any human inclination to tears. In all honesty he had thought himself incapable of tears since there had been none at the destruction of his planet or for the loss of his mother.
Not that he hadn't grieved both losses deeply; he had. The grief he'd felt still roiled beneath his enforced control, like a great tide wearing away at the shore. Perhaps that was it. The grief he was always carrying within him had finally overflowed in the face of the loss of the only man to ever call him friend. It was a simple answer and, ultimately, a dishonest one.
Spock didn't want to lie to himself; he'd done that enough in his life prior to the destruction of Vulcan, and if he'd learned anything from that loss he had learned to accept his emotions even if he then chose to suppress them.
When he was looking at the Captain—Jim—through the glass, he had felt so many things he had nearly been overwhelmed—frustration, affection, grief, and love. He had known in that moment that his feelings for Jim were more than duty, more than friendship, more than anything he'd ever experienced in his life. In that moment he'd known that his entire life would be diminished by the loss of this one man. He had been devastated and had turned to that primal anger that all Vulcans feared in order to survive the raw pain he felt.
But now that Jim was back, he had to decide what to do. It was one thing to accept that he loved his friend, but it was another to allow that emotion to change anything else about his life. The most logical option was to erect the proper walls in his mind and begin the long process of purging the emotion. There were many reasons to do so. Jim was his commanding officer and as such any relationship between them would be seen as inappropriate by many, and there was also his relationship with Nyota to consider.
Spock conceded that his relationship with Nyota was outside the bounds of logic as well. Technically he was her commanding officer, like Jim was his, and considering the status of his people, the logical thing to do would be to marry a suitable Vulcan woman and attempt to have as many children as possible. However, at least with Nyota he could still have children to carry on his Vulcan genes. That wasn't possible with Jim.
Nyota was smart, courageous, and understood his culture like very few humans did. Continuing his relationship with her was the most logical course of action. He did care for her, and he knew that they could have a successful and productive life together.
But it wasn't what he wanted. Not anymore. His father's words rang in his ears: "You once asked me why I married your mother...I married her because I loved her." And Spock knew that he would accept no less in his life. If his father was brave enough to follow his heart, how could Spock do any less? He did not ever want to tell a child that he'd married for logic and not love. It seemed like a disservice to the memory of his mother to do so.
Having found the peace that acceptance brings, Spock turned his attention to his other emotions, burying the anger and strengthening his control. When he was done he would speak to Nyota and then return to Jim's bedside. He knew there was no guarantee that Jim would feel the same way about him, but that didn't matter. He would be there for Jim for whatever he needed—friend, brother, or lover.