AN: I have already dealt with the more serious ramifications of this episode in several different, much longer stories, so I think we're entitled to a less traumatic one more in the spirit of the original.
For sake of reference, we assume that McCoy successfully hides the forced mind-meld from everyone for at least an undetermined period of time.
Spock suspects the imposture the instant the captain steps off the Enterprise's transporter pad.
This is not due to some strange, instinctive emotional recoil on his part, although there is that, upon reflection; but rather, because while present society is one of relative equality, a peculiar quirk that the captain possesses is a somewhat old-fashioned sense of deferential chivalry which typically endears him to others, particularly to the females of many species. Simply put, the James Kirk which Spock knows, would not brusquely push past his communications officer in the manner that this human did after materializing, at least not in the absence of a red alert.
The James Kirk he knows would also not react with distrust toward any crewman simply based upon the appearance of youth, especially such puzzled officers as the trio of young Engineering ensigns they pass in the corridor. The James Kirk he knows would not carefully look around each corner before moving further, as if constantly waiting for an ambush. The James Kirk he knows would not, Spock believes the most accurate phrase is, leer suggestively at least twelve (thankfully unsuspecting) crew members on the way to Briefing Room One.
The James Kirk he knows would not refuse his fourth cup of coffee of the day from a suitably mystified yeoman.
Obviously, the man is an impostor.
In an interesting, if somewhat less important, side note: neither would the James Kirk he knows attempt a full eight times to break out of the Enterprise brig's holding cells, not one of said times making it past the secondary force-fields before being stunned into unconsciousness yet again by the much-entertained Security guard at the end of the corridor.
Determination is obviously a (mirror) universal constant; common sense is quite obviously not.
However, they have far more urgent matters to attend to, and likely limited time in which to do so; Spock spares the imposters no more thought until the last five minutes prior to their intended cross-universal transport.
His calculations for artificially replicating the storm conditions are perfectly sound, though he would prefer to have them checked by Montgomery Scott instead of the Enterprise computer, even if there is no real logical reason for this. But it is the variable factor which gives him most pause. Blindly assuming his parallel counterpart will have also completed the required actions on the other end of the transport corridor means that chances of their success are extremely small; small enough that he knows better than to actually calculate them, as logic would dictate there is no logic in making such a foolish attempt on so little data.
He should perhaps have made more progress on a contingency plan to be implemented in the case of failure; because if they do fail, they likely will never have a second opportunity for success.
However, in the truly characteristic defiance of all logic which seems inexplicably to bestow fortune on this ship, the mirrored landing party is successfully sent into the artificially ionized transport flow, still cursing and protesting; and their own landing party is as successfully separated from it. Quick, painless, and relatively easy – so easy, in fact, that it is highly suspicious.
(It is only months later, that Spock realizes his reservations were indeed well-realized, and that his mirrored counterpart is far more dangerous, at least to anyone not his captain, than Kirk clearly thought him to be; but at this time, Spock does not have that knowledge.)
Relief is a human emotion, but the cause is sufficient. All is well.
Immediate ship's business having been satisfied and the landing party cleared by Sickbay of any potential pathogens from their journey into a harsher universe, Spock has no objection to delaying a full report on the trans-universal transporter malfunction to Starfleet Command, when the tired suggestion is made two hours later.
All four landing party members, in fact, are clearly showing signs of stress and exhaustion, as it has been a tiresome day and night on top of two additional days of equally tiresome negotiations with the uncooperative Halkan council on the planet below.
Dr. McCoy in particular seems unusually unsettled, though according to his initial report there certainly is cause; working in the mirrored Sickbay was clearly a horrifying experience in many aspects, and it would have been emotionally disturbing for a human physician who observes his Oath. And while it seems that Lieutenant Uhura had been in the most physical danger close to their exit, Spock has also seen the lieutenant quite capably defend herself more than once; she does not seem unduly troubled by the situation, like the competent officer she is. She will undergo a psychological evaluation alongside the rest of the landing party tomorrow, but she assures him and Nurse Chapel meanwhile that she is quite well, physically and mentally.
Montgomery Scott appears to also be in reasonably good health, and in fact quite cheerfully offers to inspect Engineering, the Bridge, and Sickbay all, top to bottom, to ensure their visitors had not left any dangerous surprises behind in the few hours they'd had access. This decided and logged, Uhura and McCoy soon follow Scott out of the briefing room, and Spock is left to retire for the few remaining hours of the night, alongside Captain Kirk.
Kirk's own initial report was exceedingly suspicious in its entire lack of specificity regarding what he had personally experienced in that other universe. To Spock, this is a clear indication that whatever it was, it is still affecting the man deeply; and the possibilities are not difficult to extrapolate, from the information at hand. There are a limited number of ways through which a captain can lead his crew; and inspiring affection and loyalty surely was not the method of the barbaric human Spock had encountered earlier today. Maintaining a charade well enough to avoid detection in such circumstances would not have been easy, to say the least.
But he also well knows that Jim will talk when he is ready, and not a nanosecond before; there is little logic in wasting energy requesting more detail at this time.
"Negative. I do not believe your counterparts were even present in public areas of the ship for long enough to sabotage vital systems," Spock says, in answer to Kirk's latest question, as they exit the turbolift onto Deck Five. "They were not successful in deceiving anyone aboard for long. I do not anticipate Mr. Scott locating any such issues."
"Well, that's something. I don't want any nasty souvenirs we might not discover until we try to warp away, for example. We're likely going to record a failure as it is with the Halkans."
"I would not term refusal to ensure compliance by force for the sake of financial gain, to be failure, Captain."
Kirk half-smiles. "Nor would I. But it's technically mission failure, nonetheless. Starfleet Command will not exactly be pleased I failed to deliver such a potentially lucrative mining contract."
"Fortunately, there is very little possibility that such failure carries the consequences your mirror counterpart threatened, earlier today."
"I won't argue with that," Kirk chuckles. The amusement fades almost immediately, however, and he swallows audibly. "Honestly? That place was absolutely terrifying, Spock."
"I can imagine it might be."
"When I think about how close we came to being trapped there, for the rest of our lives…even if that was likely to be extremely short, all things considered…" Kirk shakes his head, as if to rid himself of a vision. "Let's just say, I am quite pleased to be home, Mr. Spock."
Spock inclines his head in tacit agreement, as they reach their doors. "Indeed. Good night, Captain."
"'Night." Kirk stifles a yawn, and then his eyes widen as the First Officer's door slides open. "What on earth – did my imposter destroy your cabin or something, Spock?"
"Negative." As it is well past 0400 hours, Spock stands aside to allow the human entry and the door to slide closed, so their conversation is not audible from the corridor. "It is simply an unfinished experiment, which is no longer of interest. I have not yet had time to dismantle the project or re-organize the working area, given the events of the day."
Kirk blinks, stumbling slightly as he avoids tripping over a data-padd and what looks like some type of machinery parts. He bends down to pick up the padd and place it out of harm's way. "I've never known you to not see an experiment to its conclusion."
"In this case, the catalyst for the experiment is no longer a pressing matter, meaning time would be more productively spent elsewhere."
"Well all right, if you say so." Kirk starts to set the padd on the nearby desk, and then pulls it closer, squinting at the schematic on the screen and then looking over the nearby debris-pile, then back again. "Spock."
"Sir?"
"I may not know as much about temporal physics as a Vulcan scientist, but I can certainly recognize the schematics for a tachyon particle accelerator and…what looks very much like a homemade temporal gravitation inverter?"
Spock does not immediately respond, as he does not know quite what is being asked.
"You weren't, by any chance, making plans to build an inter-universal transportation device with a stabilized ionic reversal field from scratch?"
"If you are aware of another way to acquire or at the least construct such a device, I should be pleased to hear it, Captain. For the sake of my notes."
Kirk smiles and shakes his head before setting the padd carefully on the desk.
"It's never been done, you know that as well as I do. Not well enough to be precise without outside factors like that storm today," he says over one shoulder as he gracefully picks his way through the clutter toward the shared lavatory between their cabins. "It would undoubtedly have taken years, even for you. Particularly working by yourself."
"As the trustworthy version of Lieutenant-Commander Scott was unfortunately in your company, I was left with little choice in the matter."
"Well, I am even more glad we made it back, then." The captain then pauses, turning around with a strange expression to lean against the wall, arms loosely folded and ankles crossed. "You know this is incredibly illogical, Commander."
"I must respectfully disagree."
"Oh you must, must you?"
"Affirmative."
"Tell me this, then, Science Officer – if the plan hadn't worked today, for how long would you have kept attempting the impossible?"
"Until I succeeded."
The simple answer seems to entirely take the man off-guard, because his eyes widen slightly, and his posture straightens on the instant, arms falling to his sides. "Spock," he says, voice strangely gentle. "I wouldn't have wanted you to do that."
Spock firmly turns off the data-padd and its somewhat damning evidence. "With respect, Captain. Your personal desires have never been, and are not, an informative factor in my scientific endeavors."
"Well, if that's what we're calling it, far be it from me to interfere with science."
"That is the most logical course."
"Mm. And if, purely as example, mind you, my personal desire would be to get your opinion on the Halkan issue later this morning over breakfast, what does science say to that?"
"That it is coincidental but fortunate that our disparate endeavors align. In this singular instance."
"Well, I do like being an exception to a rule."