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Sure, Jim was shocked as he watched the kiss between Spock and Uhura - he hadn’t exactly seen that one coming - but he was more feeling jealous. Contrary to what a lot of his classmates would have believed, he wasn’t jealous of Spock because he was kissing Uhura, he was jealous of the two of them together. Despite everything else going on, the two of them obviously cared about each other and were throwing caution to the wind with what might be the last time they ever saw each other.
Jim knew he cared about Bones, and he knew Bones cared about him, but for the tiniest of split seconds he wished that Bones wasn’t the most experienced medical professional on board so that he could be in the transporter room with him. Never mind the lecture he knew would probably come as well, the kiss accompanying said lecture would make it all worth it. Well, he thought to himself, if there was ever a damn good reason to make sure he came back alive, Bones was it.