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It was published in the print zine Out of Bounds: Gypsies, Tramps and Thieves.
"When McCoy mistakenly thinks Spock is raping Kirk when he accidently sees them making love, it makes it harder for him to accept the situation when he learns the truth.."
Reactions and Reviews
Terrific angst-filled beginning when a drunk McCoy stumbles upon the partially open door of Kirk's quarters and sees the two engaged in a late night, extremely hot lovemaking that McCoy interprets as Spock raping Kirk. Despite Kirk and Spock's best efforts to persuade McCoy of their love for each other. McCoy becomes embroiled in his negative and angry feelings. I thought McCoy's emotions were very well-portrayed and believable in his denial. All this is also very well-written and an excellent characterization of McCoy. The only minor flaw was some confusing parts where I couldn't tell if they were thoughts, dialogue or narration... There are some really good lovemaking scenes and I have to say I enjoyed this story a great deal. So even though it's really McCoys story, (and a confusing title) it's definitely one to read. 
Domestic Affections takes a stock incident in our fandom—McCoy discovering the sexual relationship between Kirk and Spock—and transforms it. McCoy does not take the news kindly. He is outraged, bigoted, insensitive, and to top it all off, stupid. He actually has the two commanding officers restrained under Security while he performs tests for their sanity, believing that it was simply not possible for Kirk to respond to his first officer in such a way unless he was either under Vulcan mental influence or out of his mind. Of course, the tests actually show the two men are even more well adjusted then previously, so McCoy is left to silently endure not only their hostility but the crew's.
The rest of the story has McCoy taking leave and visiting Georgia. We get to meet his ex-wife and daughter, and get a glimpse of why he left Earth for Starfleet Then he returns to the Enterprise, and the question is whether he can patch up the relationship with his two former friends.
The story is written by Janet Alex. I believe that's a pen name for Joanna Russ, who is a professionally published science fiction author. There are several incidents that are really just too hard to believe, including the very first scene where a drunken McCoy just happens to be wandering the corridors at 4 a.m., and he just happens to pass the captain's quarters where the sliding door has been stuck open, and the mirror in the quarters just happens to show a view of the two lovers in bed together with what looks like a rape of Kirk by Spock in progress.... Right there a reader knows a serious suspension of disbelief is needed. Likewise, the incident that transforms McCoy's attitude parallels his own situation so closely that one can only shake her head at the coincidences in the universe.
But if the details of this story are hard for me to swallow because they are occasionally unlikely, the emotional integrity rings very true, and that's what makes Domestic Affections a story I like to re-read from time to time. A McCoy who isn't supportive, who reacts with confusion and jealousy is a pleasant novelty. The relationship with his ex-wife also is realistic, the desire to reawaken old passions, the reruns of arguments. There's an exception, though. Early in the story there's one scene where Spock makes an attempt to make the doctor understand about him and Jim, and he seems much more openly emotional than I can believe.
The story ends with a very satisfying sex scene. I've often thought that the author understands the desires of the typical K/S reader, since it would have been quite simple to end the story on page 27 and the scene before; it even has the requisite tag line. But the story would not have been nearly as satisfying to me as a K/S reader without a glimpse into the intimate sexual lives that Jim and Spock now share, and upon which the story is really focused. Domestic Affections revolves round and round the vision of Jim and Spock in bed that McCoy glimpses in that first scene. It makes for a complete story in both structure and emotional satisfaction.This zine is now in the K/S Zine Library. I recommend it!