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Bones was the first one to find out. It was an accident, really. They were just having a normal lunch conversation when it slipped out.
"Jim, I mean this in the nicest way possible but you look terrible."
"I didn't exactly get much sleep Bones. Spock kept me up most of the night."
Bones started to choke on his potatoes. Kirk pounded his back until he was alright. Once Bones regained his composure, he said in a straight voice, "Jim, please tell me you mean you were going over the plans for our next mission."
Jim, realising his slip-up flushed bright red and suddenly couldn't look his friend in the eye. All he managed was a weak, "Um..."
Bones groaned. "You and that pointy eared bastard are sleeping together? And you didn't think to tell me this? How long has this been going on?"
"Keep your damn voice down! I don't want the whole ship to know!" whispered Kirk. "And about three months, not that it's any of your damn business."
"Three months!" cried Bones. "And you never thought to tell me this?"
"We agreed not to tell anyone. It's not professional," mumbled Jim defensively.
"I'm supposed to be your best friend, Jim! Don't I get to be an exception?" Bones said.
"Well I guess it's your lucky day because my ass is so sore that I can't watch my mouth."
"Jim, do me a favour and never mention anything like that to me ever again."
"Wait, so you don't want to know about the time that we..." Jim started.
Bones slapped his hand over Jim's mouth, glared at him, and said "No."
When Bones released his hand, Jim was smirking.
"Oh this is gonna be fun," he said.