...Exchange the captain with his alternate from another universe.
The evil/alternative/mirror captain, -for all that it was somewhat-kinda-disturbing to imagine an evil Kirk, let alone to see it- did not perturb the crew overly much.
Nor did the other Scotty, though everyone was happy to learn that even from another universe, Scotty kept his taste for sandwitches of all sorts. Some things do not change. Some things do not need to change. And the fact that mirror Scotty still had his "Secret-Alambic-That-of-Course-Did-Not-Exist-Officialy-Because-The-Captain-Would-Need-to-Forbid-It-But-The-Captain-Was-Quite-Okay-With-Its-Non-Official-Existence-As-Long-As-He-Could-Enjoy-Its-Results-And-Even-The-Vulcan-Commander-Knew-to-keep-His-Eyes-Closed-On-It-Sometimes-Literally-And-Wasn't-It-The-Coolest-Thing-Ever", well, that this was the same in the other universe quite reassured them. Finding some universal constant was nice. Even just in booze and sandwitches. Particulary in booze and sandwitches.
Mirror-Uhura, for her part, was too sexy for most of the crew to be overtly deranged with her, particulary since they all departed before she could do anything too un-uhuraic. (Like killing or torturing someone. The way she verbally cut down this one ensign who said this sexist commentary on her wardrobe-aka-ISS Uniform while flipping him over and somehow simultany sending her heel in the more sensible parts of his anatomy was considered quite on par with what their Uhura could have done. Well, maybe with a little less physical violence, but it was still deserved and not wholly unexpected).
And the mirror redshirt did not even registered.
Come to think of it, they even kept the new guy whose bigest dream in life was to have an average peacefull life while regaining their own innocent little redshirt who was quite happy to get a twin with the same goals for life in mind. The commander just had a look in both heads to verify that yeah, they were genuine in their desires and that was all that was to be said on it.
Mirror Scotty, for his part, was more than satisfied to exchange alternative redshirt for a neutered tribble and his weight in sandwitches (after all, something needed to be send via beaming system and as far as alternative-Scotty was concerned, common redshirts who did not belong to engeneering, particulary security redshirts, were disposables, sandwitches were not). No one knew if Mirror Kirk even noticed.
Of course, the same could not be said of even just the idea of an evil doctor McCoy. This detail, this mere possibility gave quite a few nightmares to a good number of people on board and only the fact that yeah, they kept THEIR doctor and the OTHER one, MIRROR McCoy did not even put one toe in their universe stopped a full panic to arise on board. Only two crew members ended with a full-blow panic attack and three dozens were in need of a calming hypo -curtesy of the nurses- but on the whole panic was avoided. And the good doctor somehow kept in the dark about the whole situation. But Mirror Kirk did not overly perturb the crew. An evil Kirk was a false Kirk. Point. Nothing to do with THEIR captain (yeah, the crew as a whole had gotten quite possessive). It was just another form of 'False-Kirk-Guy-With-Surgery', 'False-Kirk-Guy-With-Portable-Hollogram', 'Metamorph-False-Kirk', except they were supposed to be more carefull in avoiding to kill the False-Kirk this time.
Normal life on the Enterprise for the regulars.
No, what ended a bit more embarassing was Nudist-Kirk, from the Nudist Universe, or Nudist-U as it came to be know.
Well, the female half of the crew actually quite enjoyed the sight, to be honest... Not that thet were the only ones, just the ones who admited to do so -at least to their friends. The exchange between Nudist-Kirk and the admirals ended being one of the most memorable of all so far, and considering the number of strange situations and interesting meetings the captain had had with the amiralty, that was something. Not just because the admirals had not been adverted that they-were-not-in-presence-of-normal-Kirk prior to the meeting, but it may have contributed to the... strangeness of the situation. And bewilderness of the admirals. Particulary since Nudist-Kirk did not find anything wrong with his behaviour and continued on with his report, seated stark naked on the Enterprise's command chair with all the old guys -and women, and not-so-old ones as well- gawking at him.
He did not like clothes. Too constricting, he said.
He also had the problem of being allergic to all kind of know tissues and fabrics in the universes and so was quite glad that his was a nudist one though considered that he had a medical exemption from wearing clothes even in other realities.
A fact confirmed by his doctor McCoy who, as grumpy as he was -some things do not change! proved to be a very nice surprise underneath his clothes for a good number of appreciative people. And made some others jealous.
No one was late for medical check-up this week... Some even came in advance. Weeks in advance. The captain -the real one, Their captain-, even suggested to do all his consultations in the nude in the future since it provided so good results (and got promptly hypo-ed as a result).
In any case, the situation provided an important source of naughty dreams for a good part of the crew. The embarassed blush that flittered between scowls on Normal McCoy's face for a good few weeks after he came back with the captain did nothing to abate them. But Nudist-Bones (pun intended. and deserved. Just ask the crew!)'s presence did a lot to convince everyone of the legitimity of this alternate universe and that No-It-Was-Not-A-Prank-But-Real.
Had it been just Kirk, it may have taken quite a few more hours for people, particulary the commander, lieutenant Uhura and the doctor himself, to accept it. They probably would only have taken it for the truth after forcing some clothes on the poor guy and witnessing the resulting allergy...
On the other hand, the lone nudist-redshirt passed totally unremarqued between those two, though his counterpart, normal-redshirt, could be recognised later in corridors or in the mess hall by the deep blush he carried on whenever he looked at anyone for months after the fact.
Oh, and of course the Enterprise just HAD to be attacked by klingons JUST when Nudist-Kirk was here. And in charge. Well, somewhat in charge. Lets just say that HE decided that he was in charge. After all, they were asking for the captain. And they knew that it was not commander Spock. Though their reaction to the Naked Captain ended being... Most interesting. Apparently klingons could choke on air and get almost-apoplexy attack just as easily as stiff-lipped starfleet admirals.
Of course, everyone on board decided to act like everything was normal and THEY were the weird ones for being surprised. After all, it was a completely legitimate Captain James Tiberius Kirk, just not quite their own… Yet everyone admited that theirs could very well decide one day to imitate his counterpart, they were okay with it and it would not be too much Out of Character for him to do so.
A formal document signed by most of the crew was even officialy registered not soon after the accident and send to the captain (three times), to the admiralty (two times), to the commander (they had to for it to be official) as well as to the administration (just the once).
After all, they had to be ready if their captain suddenly developed his counter-part allergies. And they were perfectly okay should the captain decide he needed to get used to being naked at work Just-in-Case. And Nudist-Kirk proved that you did not need to wear clothes to be efficient, as proven in his dealing with the klingons. Or at least, he did not need them. It had to be noted.
Besides, the real captain also had to work with a Nudist-klingons attack in Nudist-U. And from the reports, he had to play the part of his counterpart quite convincingly. Which, of course, can be translated by a quite figurative "when in Nudist-U, do as Nudists do". Something that gave quite a few people dreamy eyes when thinking about. And had quite a few hackers do their best to crack into the system just to get their hands on this report, because damn it, it even had a couple of videos and it was not fair only highter-up would get to enjoy it. (or future generations, when the archives would finally enter the public domain.)
Vulcan-Kirk was by far the weirdest Kirk. Yet not.
Quite in touch with his non-existent human half, "logic demanding that he adapts his behaviour to that of those under his command, comprising mainly of humans, and didn't IDIC embrace all that was in existence? Infiny Diversity in Infiny Combinations was after all supposed to be the vulcan way and what humans would call his motor of life. He was only following the vulcan concept to the letter".
The resulting not-clash and discussions (not arguments, never arguments) with mister Spock ended being... Quite fascinating. To coin a term.
Extremely talented in twisting words and verbaly logic himself out of any kind of situation, Vulcan-Kirk had managed the art of being, in his own words "logically illogical and illogically logical when needed" and since he was, in his way, "following the concept of Absolute Logic if sometimes Logic of the Absurd", he could, in a "disturbingly logical way" (Sulu's words), be seen as a perfect exemple of Vulcanicity (if the word existed).
Needless to say, commander Spock was most diligeant in getting their captain back.