Spock has been keeping a secret. He is not comfortable with it, but he finds it necessary.
He is in love with his captain.
In reality, he has had this secret for a long time. He first came to the realization that he felt love for his captain as he witnessed his death in the warp core.
Even after this realization, and the relief that Jim’s demise was temporary, Spock chose to continue his relationship with Nyota. He cared for her. It was not the same devotional love he felt toward Kirk, but he knew that was a lost cause, so it seemed there was no harm in continuing to see Nyota.
When it became more troublesome to continue to watch his captain pursue others, Spock sought solace in the idea of doing his duty and resigning from Starfleet for New Vulcan.
He advised Nyota of his plans and their relationship ended.
And then Krall and Altamid happened.
For a while, Spock allowed his relationship with Nyota to resume, given that was what she seemed to wish, but the distance between them grew, they both felt it, and finally she came to him and asked to remain friends only.
Spock had been relieved. He hadn’t wished to lose her, he just didn’t care for her the way she deserved, and they both knew it.
Spock continued to keep his secret, while keeping a watchful eye on his beloved.
He was pretty sure he hid it well, until one day, after Jim was injured yet again in a mission, and he kept a close eye on his recovery, McCoy came to stand beside him as they studied their unconscious captain.
“You should tell him.”
McCoy sighed. “Spock, stop hiding behind your Vulcanness and tell him how you feel.”
“I have no idea what you are talking about.”
“Sure. Only the longer you wait, the more chance he’ll give up entirely and find someone else. It’s already been close. If you don’t act, Spock, well…it’s your funeral.”
“A perplexing one.”
“Just…do it. Even if it’s while he’s sleeping. Get it off your chest.” McCoy sighed. Pinched his nose. “Another expression. I gotta go check something.”
And McCoy walked away.
Spock had no idea why he let McCoy talk him into this, but he walked over to Jim’s biobed. Stared down at his unconscious form.
“I am in love with you,” he said, softly, pushing a lock of hair off Kirk’s forehead.
He turned and left.
After Jim was released to go to his quarters for further recovery, he called Spock to see him.
He smiled when Spock arrived.
“Hey. You want to play chess or something?”
Spock agreed. It seemed as though his secret still belonged to him.
They were in the middle of the match, when Jim leaned back.
“When were you going to tell me?”
“You know what.”
“No, I am afraid I do not.”
Jim sighed heavily. “I wasn’t asleep.”
Spock blinked, stared. “I see.”
“And for the record, I’m in love with you, too.”
A better outcome than Spock had ever expected.
Much later, when they were lying in bed beside each other, having done quite a bit of exploration, Jim turned to him, put his hand on Spock’s face.
“So. When were you going to tell me?”
“When it became relevant.” Spock paused. Smiled slightly. “As it just did.”