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Spock was immensely relieved and grateful that Doctor McCoy had somehow managed to raise Jim from the dead. But even though Jim was alive again, something had changed about him, enough that Spock still felt a sense of immeasurable loss.
Jim wasn't himself, which in a way was to be expected. He had died, after all. At first Spock had assumed that Jim's quiet despondency was a result of being forced to come to terms with his own mortality. But as the weeks went by, Jim showed no signs of changing, no sign of getting better.
Worse still was the matter of their bond. Before Jim had died, he and Spock had been bonded. Neither of them had been aware of it, at the time. It had formed spontaneously at sometime earlier. But Spock felt the tearing feeling in the bond centre of his brain when Jim slipped away in that chamber. It was the same tearing Spock felt when his mother died.
He hadn't been aware of the bond when it was there, but now that it was gone, he couldn't ignore its absence. He could feel the remains of the severed bond reaching out, searching for someone. Searching for Jim. Throughout Jim's recovery, Spock stuck to his side, often holding his despondent bond-mate— ex-bond-mate's hand in hopes that the broken bond would be able to find Jim again.
But no matter how much time passed, the bond did not reform. It was as if the severed bond didn't recognize Jim as its other half. It was as if Jim had become a different person entirely.
They grew apart as Jim completed his recovery. He returned back to duty as captain of the Enterprise, but he never returned back to his usual self. The crew noticed the changes, and they seemed unsettled and saddened by them. Jim was still kind to them, but he never stopped to really talk to anyone anymore, and his smiles were polite but unnatural. He floated around the ship like a spectre, always seeming like mentally, he was somewhere else. And if you looked into his eyes, you would find an emptiness behind them. His crew didn't make eye contact with him anymore.
Spock waited, illogically hoping that one day, Jim— his Jim, would suddenly come back to him. But as the weeks and months passed, he became less and less hopeful. In the end, his flailing and perpetually searching bond fragment grew weaker and weaker, until it shrivelled and died, taking Spock's hopes with it.