It's the eyes that he found slightly unnerving. Well, as much as a Vulcan could ever find anything unnerving.
The elder version of Spock could scarcely believe that he had been so quickly reunited with this time-line's Jim Kirk. He knew the man's shouts, his movements, the outline of his face the moment he grabbed a flaming torch and chased one of the many monsters of Delta Vega out of his refuge.
At first, Kirk had been looking down, trying to catch his breath. But when he looked up … that's when it became apparent to Spock how radically Nero's appearance had altered this time-line.
Piercing blue eyes stared back at him warily. Spock had only met one other person in Starfleet with such a clear blue gaze, and it was not Jim.
As he sat waiting to be picked up in the Starfleet outpost on Delta Vega, he wondered at the difference. Although he tried to only broadcast one particular line of thought to this new version of Jim during the mid-meld, he could not help but feel a mind full of deep-seated pain and anger that his Jim never had. This Jim was younger and brasher. In his time-line, they had not yet met at this age. Spock was able to contain his surprise when he looks up his friend's file in this reality, and wonders at the probability of two completely different story lines weaving themselves together to create two versions of the same person. Apparently Nero's presence had changed more than he realized.
It was only much later, once he had returned to Earth and revealed his existence to his younger self, that he started to wonder whether this was more than just a case of altering a time-line.
Before long, he had met most of the command crew in this reality. There were subtle differences: Lt. Uhura wears her hair much longer, Chekov has curly hair, Sulu looks just a bit taller. Finally, he approached Dr. McCoy from behind as the doctor entered commands into a computer terminal in medbay. He seemed nearly the same as his counterpart, with the same drawl gruffly calling out orders. Then he turned around.
McCoy took one look at the older Spock and bit his lip, debating internally whether he should speak his mind. Spock tried not to smile at the uncharacteristic restrain of the doctor, then takes a closer look. McCoy's eyes are dark, almost the color of his Jim's, but Spock can see instantly that they still convey the same range of emotions that he could read in his McCoy's eyes.
"Please, Doctor," the older Spock says. "Say what it is that you wish to say."
McCoy accepted the invitation without question. "Damn it, as if one green-blooded hobgoblin on this crew wasn't enough, there has to be two of ya!"
"It is good to see you again as well, Doctor," Spock replied warmly, feeling the absence of his own crew acutely. The doctor's eyes softened; there was the genuine care and concern so often masked by annoyance and exasperation that Spock remembered in another pair of blue eyes.
In his quarters that evening, Spock pondered the problem. This time-line's Jim had slightly lighter hair than his – perhaps due to luck of the genetic draw or spending his first few weeks in space. However, the doctor would have been born several years before Nero came through the black hole. If these minor differences were truly due to alterations in the time-line, then the doctor should still have blue eyes, as well.
It appeared that the singularity not only took them back in time, but also to a parallel universe. Even though it is illogical, Spock now felt even farther from his rightful place in time.
For centuries, scientists and philosophers had pondered the existence of an infinite number of universes representing the various outcomes of any choice ever made; differences between them could be major or minute. In light of this revelation, Spock tries to find comfort in the fact that the crew of the Enterprise are meant to be together regardless of universe.
This crew adopts him as one of their own. He plays chess with this Jim, always careful not to reveal things he should not. He provides guidance for his younger self about dealing with life among humans and an enthusiastic, vibrant, impulsive captain – advice he himself received from his mother.
However, every time Kirk or McCoy looks at him, it is a sharp reminder that this is not where he is supposed to be. These are not his crew, but another incarnation. As happy as he is to have a second chance to see his long-dead friends, he cannot forget that those he knew died many years ago. It's all in the eyes.
FIN.***************
I've only come to Star Trek fandom with the new films, so please pardon any mistakes. Much obliged. I don't own 'em, just play with 'em.