Prompt from the kink meme: Five Times Kirk Walked In On Bones and Spock Having Sex (And One Time He Joined Them). Would love if one time was during Pon Farr, which of course Kirk would have never heard of before. Not the first time, though, if you'll indulge me :-)

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One:

It was the first time for all three of them.

And of course, it was tension-induced. McCoy, for once, the injured party with a mysterious but probably treatable (if he were on the Enterprise) disease, was trapped on a planet's surface with Sulu. Spock and Kirk were both going crazy—in different ways. As soon as McCoy and Sulu were beamed back up, Spock took over McCoy's medical treatment, nearly ripping the emergency medical kit out of Nurse Chapel's hands. As soon as Jim had finished debriefing Sulu he went to join McCoy and Sulu in the medical bay.

Which was locked.

He overrode the command and entered, concerned. Immediately he heard the noises coming from McCoy's office. He stood stock still, listening with all his might. The sounds were rhythmic and fleshy. Grunts and moans were heavily peppered amongst the thrusts. Kirk could hear the intensity increasing; the noises were faster, more urgent. And then, McCoy screaming Spock's name, so loudly his voice would be raspy for days more.

Silence. Then, Spock, quietly saying a single tender word: "Leo."

Kirk fled.

Two:

For a very long time, they were not obvious. No matter how hard Kirk watched, he saw no hint of their relationship continuing. In fact, it had not—Spock had had a breakdown afterwards. He felt that he was incapable of dealing with what had just happened. In truth, Spock had forced himself on McCoy; McCoy had not at first been entirely receptive to the Vulcan's advances. He had literally warmed to Spock. For some reason, the moment Spock thrust inside of him, all traces of doubt were gone. And McCoy wanted that feeling again.

Spock went out of his way to avoid McCoy. He did not make eye contact with him for two months and would not come within three feet of him for nearly a year. Then one night, McCoy reread his favorite book, a novel about taking your chances where you can. He walked to Spock's room and knocked on the door. When Spock appeared at the entrance, McCoy threw himself on his first officer and bore him into bed.

This time, McCoy was in charge.

Three nights (and eighty-six orgasms) later, the happy couple were spending their break in a supply closet that Kirk needed some helicase canisters out of. Kirk yanked the door open to find McCoy's dick precariously near Spock's mouth. There was a moment of absolute silence.

Then Kirk slowly backed out and closed the door.

From within, he heard an actual giggle slip from McCoy. It was followed quickly by a gasp.

Three:

Kirk avoided both Spock's and McCoy's room after that, especially after the two of them (obviously spurred by Spock, considering how uncomfortable McCoy looked) descended on Kirk and tried to explain what was going on. Kirk withdrew himself from the situation as quickly as humanly possible and the subject was never brought up again.

At least not until two weeks later, when goddamn it, Kirk needed carbonite canisters out of the same supply closet, and sure enough, they were there again, only this time it was McCoy's mouth that was precariously close to Spock's dick.

Kirk let out a very quiet roar and slammed the door on them. He strode away too quickly and loudly to hear any more noises from inside.

But he couldn't help giving in, for the very first time, and finding a bathroom to jerk off in. As he came against the door, he thought of McCoy's hands, and Spock's eyes, and their mouths, together, two as one.

Four:

Five months later, Spock began acting very strange. He requested three full days off from work and would not answer Kirk's questions about why. McCoy approached him after Spock had retreated to his quarters and told Kirk that Spock really, really needed this time off, and he would do better not to ask any questions.

The next day on the bridge, as McCoy briefed Kirk on the state of the medical supplies, Spock came striding out of the turbolift and up to McCoy. He grabbed the CMO's head and planted the deepest, most fierce kiss Kirk had ever seen. The crew looked half horrified, half fascinated. Kirk leapt up immediately and ushered them out, not knowing what was happening but not willing to wait for the whole crew to see even more than they already had. McCoy, bright red not just from embarrassment, hissed his thanks to Kirk, who smiled distractedly, a bit caught up in the gigantic bulge in Spock's pants. Kirk, the last one out (not on purpose, of course, of course), turned to see Spock actually rip McCoy's clothing off of him.

Needless to say, Kirk came again and again that night, bringing himself as he imagined Spock violently taking McCoy. Kirk's grip was like death, and his forehead hurt the next day from the crease in his eyebrows.

Five:

Shore leave on an idyllic, tropical planet. Strangely, nothing went wrong the whole time, unless you count Kirk discovering that his bungalow's backyard shared a hedge with Spock's, who had McCoy over most of the time. Over the patio furniture, it sounded like, from the half-disguised moans and gasps and grunts. Kirk accidentally-on-purpose came to get Spock for a pseudo-emergency and was rewarded with Spock composedly wiping the lube on his hands off on a nearby towel while McCoy tried to look innocent in the background.

Six:

The ship was quiet.

All Kirk could hear, could concentrate on, was the beating of his heart. He tried reading, catching up on paperwork, bothering Chekov and Scotty, sparring with Sulu. Nothing worked.

McCoy and Spock where nowhere to be seen.

I can't take it any longer, Kirk thought, and before he could stop himself, he was at Spock's door, overriding the lock with his captain's code, and walking in.

The door slid shut behind him. The room was dark, and silent but for heavy breathing.

"Captain." Spock's voice seemed to come from all around. "Is there an emergency of some kind?"

The last vestiges of Kirk's sense of humor conspired to say, In my pants, but Kirk did not speak. Or, could not.

"Captain," repeated Spock still invisible. "Why have you entered my quarters?"

"Dammit, Jim," Kirk heard McCoy sigh. "What is it?"

"I don't know," Kirk managed to mumble. "I just." He paused for a long time. "I just can't stand it anymore." His voice was thick.

And then, to his absolute shock, he felt a hand on his. Soft lights came on. Spock, half-clothed, was standing close to him, his fingers resting on Kirk's wrist.

"Captain," said Spock, his deep eyes wide. "Jim."

Kirk nearly sobbed.

The expression on McCoy's face could almost be called tender.

"Bring him to bed," he said to Spock, and Spock led him in.

They bore him down, pressing against him, hands everywhere, bodies everything, until all Kirk could be was part of McCoy and part of Spock, until all he could think were their names.