Note: I recently rewatched The Original Series and my thoughts turned into this series of short episode responses. As I wrote, the individual scenes came together into a broader narrative that ties together all of the individual episodes into an arc that tracks the development of Kirk and Spock's relationship and Spock's character.
This is supposed to be approximately in continuity with a few fics I wrote in the beginning of my rewatch and posted before I knew I would be writing enough for a whole series. "A Hidden Personal Thing" and "Not Chess, Mr. Spock, Poker" occur before the beginning of the first chapter, and "Dig in There, Mr. Spock" takes place between the second and third scenes of the first chapter of this fic.
"Frustrated, Mr. Spock?" Captain Kirk asked as he took Spock's queen. His eyes shone with mischief and his voice had a very human lilt.
Teasing was what the humans would have called it, but Spock could see an uncharacteristic smugness in the captain's smile, as though he had caught Spock doing something he wasn't supposed to. For all the humanness of the gesture, the only thing Spock could think of were the sharp eyes of the Vulcans, appraising him, searching for any sign of human emotion. He could hear the implied accusation: "Your behavior is illogical."
He straightened his posture, his lips pressed into a thin line. His eyebrows rose in disbelief. There was only one way to respond, "As a Vulcan, I am incapable of feeling such emotions."
He did not expect the captain to grin, to smile at him as though inviting him to share in a private joke. He did not expect the captain to rescind his accusation without a second thought, "Of course, Mr. Spock. I must have been mistaken." His intense gaze showed only amusement and appreciation.
Spock quirked an eyebrow at him and the game went on.
"Check," Spock declared some turns later, bringing his rook forward.
"A very logical move," the captain remarked. He glanced up from the board to give Spock an open smile.
The gesture was, with high probability, a deliberate one. It was a human practice to apologize for a perceived slight with a compliment, however Spock detected no dishonesty in the captain's words - to say such a thing without meaning it would have gone against his character.
So, Spock replied, "Why, thank you, Captain."
The captain turned back to the three-tiered chess board with a wry smile. "You may not be capable of feeling frustration, Mr. Spock, but you make one frustrating opponent."
To his surprise, even after forcibly taking command of the USS Enterprise and steering it to the forbidden planet, Talos IV, Spock was not sentenced to death. He was not court martialed or even relieved of his post. Fortunately, Captain Kirk also evaded punishment for actions that were not his own.
However, Spock had violated Starfleet regulation, disobeyed his captain, and endangered the crew. Therefore, as was his duty, he reported to the captain's quarters to resign.
To his surprise, Captain Kirk shook his head. "After all that, I'm not losing my first officer," he said with half a smile.
"But sir," Spock began to protest.
"I do not accept your resignation," Kirk said sharply. His tone brooked no argument.
Only then did Spock relent, still astounded that the captain trusted him after all Spock had done to betray him. But if those were the captain's orders, he would not disobey them. Spock gave a sharp nod. "Thank you, sir," he said, and was about to turn to leave.
Suddenly, Captain Kirk asked, his voice quiet and measured, "What was it like serving under Captain Pike?"
Spock looked the captain firmly in the eyes and answered, "He was efficient and very professional."
Kirk smiled at that with a twinkle in his eyes. He was a very efficient captain, but upon reflection, Spock conceded that he would not call Captain Kirk's demeanor professional; friendly was more accurate.
Spock continued, "He expected those of us under him to do our duty effectively and did not interfere unless something was amiss."
"Did you spend much time with him?" Kirk asked almost casually, but he was clearly getting at something.
Spock gave a slight shake of his head. "I only encountered him in the course of duty and we only spoke when it was essential to our work. Despite his emotions, his approach to captaincy was very similar to what would be expected of a Vulcan."
Kirk nodded in thought. He met Spock's eyes and said seriously, "It was a very kind thing you did for Captain Pike, but don't pull anything like that again, not for me or anyone - that's an order. Understood?"
"My apologies, sir," Spock said, "But I cannot obey that order. It is my duty to ensure the safety of my superior officer."
Kirk frowned and let out a sigh. "I was afraid you'd say that."
"Sir?" Spock asked, an eyebrow raised.
The captain just shook his head.
"I believe I have underestimated the difficulties of command," Spock remarked as he advanced his rook.
Spock was sitting across the desk from Captain Kirk in the captain's quarters, a three-tiered chess board between them.
Jim, as he preferred to be called when they were off duty, grinned at Spock and moved one of his pawns. "You're not rushing to take over then?" Jim teased.
"I would be unqualified and unprepared," Spock answered firmly.
Jim's smile softened. "Bones told me what happened down there."
Spock refused to look away even as he awaited the well-deserved reproach.
"He said you rubbed the crew the wrong way, but when it came down to it, they wouldn't have gotten off that planet alive if not for you." He was looking at Spock with kind, almost wide eyes, like he had done something incredible.
"Two men died because of my decisions," Spock said.
Jim leaned back in his chair, the game of chess momentarily forgotten. His smile turned rueful. "I wish I could just say it was despite your decisions and that would settle it, but I know it's never that simple. It never feels that simple."
He sighed and looked away from Spock, no longer able to hold his sharp gaze. "It's my fault as much as yours; for getting you stranded, for the deaths of those two officers who I sent down with you on the shuttle and the man I sent down to search for you. And for all that, it could have easily been much worse. I don't know what I would have done if I'd lost you - and Bones and Scotty too."
"You performed according to your duty," Spock insisted, trying to meet the captain's eyes.
Jim just shook his head. "Maybe the Commissioner was right. I shouldn't have sent you out on such a dangerous mission when we didn't have enough time-"
"You did not know that the malfunctions would occur," Spock interrupted.
"What would you have done?" Jim asked with a small smile. Against all reason, he appeared to be open to Spock's suggestions.
"I am hardly qualified," Spock protested.
"Humor me," Jim said. "It's your duty to advise the captain, after all."
"I cannot know because I am not currently in such a position and do not know all of the constraints." Jim made to interrupt, but Spock continued, "I doubt I would have disputed the judgement of a Vulcan commissioner. A Vulcan would have accurately weighed the risks and benefits and acted accordingly. It is unlikely I would have found logical fault with their decision. As Commissioner Ferris is human, however, he makes human mistakes."
"Vulcans make mistakes too," Jim cut in, but he appeared to be amused rather than insulted.
"Certainly, however I am more likely to make the same logical mistakes as Vulcan rather than illogical human ones. Despite Commissioner Ferris's urgency, when we encountered the quasar-like formation, we were three days away from Makus III and the rendezvous would occur in five days no matter when we arrived. Exploration is the purpose of our mission and we are under acting orders to investigate all quasar-like formations. These orders do not indicate that we must do so immediately, but as the opportunity presented itself to us, it would be most efficient to do so before we received additional orders. The initial risk estimates were low, so I believe I would have made the same mistake."
"However," Spock remarked as an afterthought, "I may not have sent two of my most senior officers and my chief medical officer on the same mission. I understand the purpose of sending myself and Chief Engineer Scott, however I do not understand why you sent Dr. McCoy on a mission to investigate a phenomenon so far removed from his area of expertise."
Jim grinned a little sheepishly. "I thought he might be able to provide some support."
Spock quirked an eyebrow at him. "I found his presence to be counterproductive."
"Another miscalculation on my part," Jim acknowledged.
Spock gave him a sharp nod. "I am unable to comprehend the regard you hold for the doctor."
Jim seemed to consider it for a moment, watching Spock with half a smile as though what he saw would have some influence on the answer. Finally, he said, "As captain, it's important to hear a wide range of perspectives. I don't have to listen to all of them, but his emotions are as valuable as your logic. For one, he gives me a good idea of what the rest of the crew is thinking and he has a strong sense of right and wrong, whether you agree with it or not."
Spock's eyes narrowed as he thought over the suggestion. "That is a logical approach, however I would be disinclined to assign much weight to Dr. McCoy's opinions on how to command a starship."
"I know," Jim said. "Maybe one day you'll understand where he's coming from."
Spock's eyebrows rose in disbelief.
Note: The first scene is intended as a prequel to several moments early in The Original Series where Kirk teases Spock about having emotions, to explain why Spock is seemingly okay with it.
The second scene is a direct aftermath to The Menagerie, and the third is after The Galileo Seven.