This is only in the ST:2009 section because I don't think that McCoy knew Kirk at the academy in canon and I really wanted to add the one with Bones' own class in there. Oh, and because Kirk was surprised by one of the Nines being on his ship in The Conscience of the King and here he knows. Otherwise, it's pretty much TOS.
The five times that James Tiberus Kirk cried about Tarsus IV and the one time he actually felt closure.
He didn't cry until he was safe at home in his mother's arms.
When it was actually happening, he didn't have time to cry. He had to stay strong for the younger ones. He and Thomas were the leaders. He had to stay strong, and he had so many other things to think about when it was actually happening.
When it was finally over, he had the chance to finally have his emotional release.
He cried into his mother's chest for an hour, and didn't cry again for a long time.
It was his first semester at the academy and one of his Professors had decided that their term report had to be on a certain disaster. "The Federation isn't perfect," he had said. "We've looked at the events of Tarsus IV, and I want your report to be on what you would have done differently had you been on Tarsus IV."
Kirk sat in front of a blank screen for hours. At the top was his name and he tried to open it in about twenty different ways before he gave up.
"Cadet Kirk, I did not receive your report."
Kirk looked him in the eye and said, "I couldn't have done anything differently."
The teacher laughed. "You're not excused from this assignment, Cadet, just because you think you'd do what Kodos did—"
"I didn't say that," he interrupted, his voice colder than ice. "I won't be handing in this assignment unless you want a blank page taking up space in your databanks. Am I clear?"
"It's worth thirty percent of your mark," was the reply. "With the way your grades are sitting, unless you get one hundred percent on the exam, you'll fail the class. Even then, I will have to report you for insubordination and irresponsibility unbecoming of an officer looking to the command track."
Jim kept his mouth shut. He knew that he wasn't in the list of survivors that any teacher could just access. He was a Nine. His identity was protected so well that the only people who could access the list of names was the Nines themselves, and only the highest ranking members of Starfleet and the Federation. There was no way to prove he was on Tarsus without having to give this man top secret access codes.
"I said that I couldn't have done anything differently," he repeated and walked out of the room. He walked, cold faced, all the way to his dorm before realizing that Bones would be there studying. He didn't enter his room, but climbed up the stairs onto the roof of the building.
His mask broke and he fell to his knees.
Cadet Kirk began to cry.
That day, ten years ago, little Jimmy Kirk was sentenced to death for being an extra. He didn't live on the colony— he was a visitor— and Kodos had said, "The lives of those who belong to this colony take priority."
He skipped classes—take that, stupid professor with the Tarsus assignment!— and when Bones came back he found his best friend drunk, throwing up in the toilet.
"Oh Jim," he said with a sigh. "What is it this time?"
Jimmy looked at him, his eye blood red and his face a disgusted pale green colour, and he said, "Leonard." That's all he said, nothing more, before he pulled his friend into a bone-crushing hug and began to cry in his shoulder.
Bones received a similar assignment for his course on treating patients having a mental breakdown. Contrary to his belief, Bones did need to know a lot about psychology to be a doctor aboard a starship because of their limited personnel.
"We had a speaker from Tarsus IV today. Didn't you have an assignment on that first year?" Jim nodded absently.
"He was a doctor on the colony, and he told us about how people reacted to extreme hunger. Breakdowns and such. He even suggested that Kodos wouldn't have done what he did if he wasn't starving—"
"Of course he wouldn't!" Jim snapped. "If he wasn't hungry, then there would have been enough food around to feed all eight thousand, one hundred, and sixteen people. He wouldn't have the chance to think he needed to kill four thousand and forty-nine people."
Bones blinks. He doesn't know what to say and is silent for a long moment before saying, "His opinion was pretty interesting, though. It probably differs a lot from any of the people whose families were executed… or those Nines— you know, the ones who were supposed to be slaughtered but got away? Only witnesses who have seen Kodos' face… I'd love to hear their opinions on it…"
"I doubt they want to talk about it, Bones. Especially not with somebody who's only interested for a professional reason… or simply curiosity. Imagine what… they" (he caught himself before he could say we) "went through, Bones."
"They were kids, Jim," Bones scoffed. "They probably couldn't fully comprehend the horrors they faced or what Kodos felt he had to do. People do it to wild animals, you know, so they don't overpopulate and then don't have enough food for the winter—"
"People aren't deer, Bones," Jim said dryly. "Children were being slaughtered." His voice broke and Jim had to leave the room. Bones didn't see him the rest of the night.
Ensign Kevin Riley. If Kirk wasn't almost sure it was him by the file, he was sure when he saw his face. Kevin's eyes sparked with recognition when he saw the Captain and he smiled. "Permission to come aboard, sir?"
"Permission granted," he said with the best straight face he could. Nobody suspected a thing. Who was to say Captain Kirk couldn't hide his emotions just as well as Spock when he needed to.
Kevin had grown. He was no longer the little boy that Jimmy would give half of his own rations to what seemed like every other meal. He wasn't the little orphan who clung to Jimmy like he was the only person left in the world.
Captain Kirk cried himself to sleep that night.
"Jim, I'm sorry," Bones said suddenly.
James Kirk raised his eyebrow to his friend. "About what?"
"What I said when we were at the Academy… about Tarsus."
"It's no problem, Bones."
"No," he replied. "You couldn't have just been… so okay with me saying that. I'm your best friend, Jim, aren't I? I know I was back then… and what I said is unforgivable—"
"Stop it," he said. "No. You're right. It wasn't forgivable. But you didn't know—"
"I was just studying it, Jim. I should have noticed. How you got such a bad mark in that class… you didn't hand in that assignment, I know it! You were piss-poor drunk and crying in my arms around the ten year anniversary of it! The way you ate… everything was there! Then the way you reacted to how I said it…"
"It's over," he replied. He took a deep, shuddering breath. He felt somebody behind him and glanced back. Spock.
"Captain, I suggest you take the next week off for emotional recovery—" Spock began, but Jim cut him off.
"No," he said. "I'm the Captain of this ship and I'm not emotionally compromised. I've dealt with it before. Kev is all right, isn't he? Everything is going to be peachy and we're going to forget this ever happened. All right?"
"Jim," said Spock. "Jim, Ensign Riley has received the same offer and has wisely taken it. It would only be logical if you too—"
"Spock, it's over," he interrupted his friend yet again. "Spock… I finally feel like it's over." Tears began to run down his face and for once he just let them flow. "It doesn't hurt."
Without hesitation, Spock pulled him into a close embrace. "Yes, Jim. It's over."