Title: Shades of Darkness
Characters: AOS Kirk, Spock, McCoy, Spock Prime, AOS Enterprise crew; TOS movie-era Kirk, Spock; TNG Picard, various from all three universes
Rating: T for movie-level language and violence
Final Word Count: TBD, about 3000 per chapter

Warnings/Spoilers: Primary plot spoilers for Star Trek: Into Darkness and Generations. Various other spoilers for various other movies and Trek universe canons, footnoted where needed; no in-depth knowledge necessary to understand story. Could be categorized as a Generations fix-it.

Secondary Warning: this is technically a WIP, though most of it is already in rough draft form, so updates will be slow but consistent. Feedback is not necessary but very much appreciated.

Summary: No one is more surprised than the newly-resurrected James T. Kirk, when he opens his eyes on an unfamiliar Starfleet Medical bay and a crew nearly forty years his junior. Meanwhile, young Jim finds himself trapped in the ghostly spirit-world of the Nexus, trying to find his way home as his crew desperately search for a way to reach him before Captain Picard can convince a confused Enterprise captain to leave that elusive Valhalla to face a premature death on Veridian III.

A/N: It's been a long time since I tried another wacko off-the-wall crossover, something just for fun, so enjoy my particular brand of madness with me if you like. No knowledge necessary of TNG really to understand the story, just review a brief summary of Generations and you should be good to go. And do remember, I am a firm believer in happy endings.

Chapter One

"And so, after Mendel's development of what is now commonly referred to as the 'emotive algorithm,' the usage of the universal translator became widely relied upon as a secondary implement in ambassadorial negotiations, due to its ability to detect the subtleties of linguistic emotives which can sometimes slip by the most observant of non-artificial mediators. Any questions over this module?"

Twenty-four pairs of eyes in various stages of everything from resignation to polite boredom blink back at her. With a silent prayer for patience to whatever deities of the universe may be listening, she presses the button on the holo-padd to change the overhead screen to the week's homework assignment. The action simultaneously sends the assignment to each student's work-padd, producing a chorus of groans and beeping of data-entries as reminders are set up on two dozen electronic devices. "Then if there are no other questions, you are free to spend the remainder of the class preparing for next week's presentations. If you intend to work with your presentation partner, please be courteous to those studying around you."

With only ten minutes left in this class period, she decides to ignore the two in the back who have obviously been playing a game on their padds for the last half of her class, because it will be their own fault if they fail and she is not here to babysit a couple cadets riding through the Academy on their parents' high-ranking uniform shirt-tails. Besides, she has learned the hard way not to judge a book by its cover; it is just possible (highly doubtful, but possible) that one of them could be their next great starship captain, despite his or her appearance.

When one of them starts coughing because he accidentally ingested his chewing gum, she rolls her eyes and revises that theory. Was she ever this young and stupid?

Not for the first time, she wonders if she did the right thing, agreeing to teach a few courses at the Academy while they're grounded here, waiting for their new assignments. Waiting to see if the Enterprise is even salvageable…waiting to see if someday the powers-that-be will figure out what really happened up there, miles above the Earth…waiting to see if their captain will even wake up, or just quietly slip away from them one day. Five weeks, since they nearly fell out of the sky but for the terrible sacrifice of James Kirk, and she still hasn't gotten used to the idea that the man was, and may still be for all intents and purposes, dead.

So here she sits, grading mediocre papers from Starfleet cadets on the Communications track for the second week in a row, and wondering if this will be her life for the next six months – because either she has to wait around for the Enterprise to be rebuilt, or take another deep space assignment, and the latter is not at all appealing. Spock has made it quietly clear he has no intention of leaving Terra until Kirk wakes up, regardless of Starfleet order or personal circumstance, and while it's a little annoying that he won't even consider following her to a different posting she gets it, really. She has no idea what sort of relationship her proud Vulcan boyfriend has with the man currently lying unconscious in Starfleet Medical halfway across the campus, but it's kind of sweet, kind of sad, and all kinds of strange. And while she knows Spock loves her and no one else that particularly romantic way – despite this, she knows that wherever he goes in the galaxy, Spock will somehow always return to Jim Kirk.

And though she probably would never have admitted it before the man had to go and die for his ship, she would much prefer to keep Kirk around too – but if it's another couple months, and the captain still is in a coma? She will go nuts, just waiting around here for something that may never happen.

Jim would never blame her for leaving, in fact would probably give her his blessing; but she honestly doesn't know if Spock would ever forgive her.

The bell rings for dismissal, dispensing these morose thoughts with an impressively ear-splitting screech, and she watches the students hurry from the room in varying stages of excitement. Hers is the last period of the day, and they're obviously eager to begin their weekends.

Lucky them.

She clears the holo-screen, and takes the next twenty minutes to finish grading the last batch of research papers the students had turned in this week, so that the grades can reach their inboxes before Friday evening. Another thirty minutes and the rest of her paperwork is done, the messages sent, the grades filed, and she can finally close up shop. Maybe she can call up Christine Chapel for a last-minute girls' night.

Only then, does she see her comm-unit has been blinking with six missed calls and a variety of messages. The majority are from the Medical wing – McCoy has tried to get hold of her in the last two hours, apparently, but there's also a couple text messages from Hikaru, who has apparently taken it upon himself to be the central clearing house for the remaining Enterprise crew's fast-moving gossip chain, while they're grounded here on Terra.

She flips open the communicator to read the messages and then nearly drops the instrument while trying to snatch up her jacket and tote bag. She's out the door in ten seconds, and halfway across the quadrangle in ten more.

He's waking up.

Also, your boyfriend just pissed off Admiral Barrett by interrupting her and telling her to finish her debriefing in writing because "urgent matters required his attention elsewhere." LOL

"Hold it!"

A firm hand blocks his entry into the ward, propelling him backward with a force that is surprisingly strong, and unsurprisingly familiar. After all these weeks spent in too-close proximity over a common target, their wary truce has mellowed into something more resembling friendly animosity than anything else, though he would never admit as much to the insufferable human.

"Decon, now, or you're not goin' anywhere near that room. No shortcuts, not when we're this close. God knows his immune system's nothing special on a good day, and this isn't one of 'em."

Spock refrains from the appallingly human habit of rolling his eyes, but he knows the instructions are both valid and unable to be circumvented; so obey he does, and within one-hundred-eighty seconds is on the other side of the decontamination sonics, uniform hat in hand and (he believes) betraying no signs of his hurried rush across the Starfleet campus. If he is fortunate, the hapless cadet he accidentally bowled over in the quadrangle did not recognize him.

"I received your message, Doctor. Is –"

"He's not really awake, yet, but he's fidgety," McCoy replies, thankfully without commenting on his own agitation. The physician gives him a knowing look as they move down the white, sterile corridor. "Looks like he's actually dreamin' now, not just unconscious, and he opened his eyes for a minute. I don't think he was actually seeing anything, but it's a start."

"You are certain –"

"His vision's been repaired from the radiation burns, yeah; tests show his visual cortex is being stimulated, it was just that he wasn't really aware." What is likely supposed to be a reassuring elbow in his side, which he ignores. "I figure it'll just be a matter of hours now before he actually comes out of it. 'Course, knowing him, he'll prove me wrong and take another month to wake up, just to be a pain in the ass."

Spock's eyebrow inclines. "That would be highly irregular, medically speaking."

A snort. "This whole shebang has been highly irregular. I still can't believe you managed to talk us out of trouble over it, Spock."

He clears his throat, uncomfortable over the fact that for the first time in his life, he has deceived his superiors outright, lying to a Starfleet board of admirals and destroying evidence which would betray just exactly what had happened aboard the Enterprise that fateful day. But he and McCoy had agreed, no one could truly know what had taken place, no one could get their hands upon the formula the doctor had developed – because the consequences of it falling into the hands of such as Marcus and Khan would be far too great. And while most of what Spock had done he had been able to excuse as lies of omission, given that Montgomery Scott and McCoy were the ones actually altering the Enterprise's data banks, the knowledge that he had successfully carried out such a deception did not sit well with his conscience.

Still, for Jim? He would do far worse, and with less conscience, if needed.

Now, they enter the room which has become so familiar over the space of the last thirty-nine days. He does not mentally name the hours and minutes, though he knows them well; for they do not matter now, if Jim is waking up – because that is what they have all been waiting for, been working for, this entire time. Everything that has happened in the last five weeks will not have been done in vain, if he wakes and is himself.

And if not? He does not dare contemplate the possibility, for he knows McCoy has already run through the frightening scenarios in his mind, and he does not wish to add to that unease. Brain-scans show clearly that the man lying in the bed is indeed Jim Kirk, and only Jim Kirk, so they should be able to rest easy in the knowledge that Khan's blood has not changed him mentally; but that does not mean there will not be long-term repercussions from this event, either traumatically, emotionally, or physically.

They can only wait.

"His heartbeat's up, that's a good sign – it's almost normal now," McCoy murmurs, almost to himself, as he inspects the monitors. "In fact, it's a little fast," he adds, glancing down at the still figure on the bed.

"Is that cause for alarm, Doctor?"

"I doubt it, just means he's fighting his way back. But I want to keep an eye on it, in case blood pressure issues result from the irradiation reversal. Whoa, that's new!"

The captain's pale face has scrunched up as if he is simply waking from a nap – Spock has caught him asleep at his desk enough times to know the look – and his head moves slightly to one side.

"That's it, Jim. Take your time, though, nobody's goin' anywhere." McCoy adjusts a monitor setting and steps back, patting the man's shoulder gently through the hospital gown.

"Doctor, how long –"

"I got no idea, Spock! I'm a doctor, not a fortune teller - he'll wake up when he's damn well ready!"

"A sound observation, Doctor, though I was hoping for a more scientific analysis," he replies dryly.

"I can still kick you outta here, you know."

His response is lost in the sudden commotion which results in James Kirk returning to consciousness as he does nearly everything else in his life – with as much drama as possible. Arms flailing like a dying cephalopod, lungs gasping for breath, startled eyes darting around the ward, he takes them both completely by surprise for a second or two before McCoy jumps into action.

"Holy mother of - Jim! Hey!" He grabs the weak hand which flops his direction and pushes its owner back to the pillow with a firm grip. "Calm down, already! Spock, gimme a hand here?"

He steps forward, and sees blue eyes shoot over the physician's shoulder toward him, widening slightly with what looks like recognition – and then the man relaxes, slowly going limp and blinking at his surroundings with what looks like weary confusion.

"Jesus, you know how to scare a man." McCoy releases the captain's wrist and glances at the heart monitor. Sees the numbers returning to a normal range, and huffs out an amused breath. He looks back down at the bed, shaking his head. "You with me now, Jim?"

Kirk blinks again, slowly, eyes traveling around the room, and then they return, fastening oddly on Spock's face for a moment. When he speaks, it's with an oddly stilted inflection. "Where am I?" he asks, voice hoarse with disuse.

"Starfleet Medical, the research wing, on Terra. Your precise location is being kept secret to avoid the intrusion of the press for as long as possible." Spock's eyes narrow as this information does not appear to bring any relief or recognition. "Do you remember the events which landed you here, Captain?"

Kirk blinks up at him, eyes strangely piercing. "Why am I in the research wing, and not the primary recovery wing?"

McCoy glances over the captain's head, meeting his eyes with a helpless look that clearly asks whether or not Kirk should be told the truth. Spock unfortunately has had enough experience to know that if not told the truth, Kirk has a habit of discovering said truth in short order, so it is more expedient to simply, as they say, get it over with the first time around.

"Because Doctor McCoy's method of…resuscitating you, involved experimental measures with Khan's blood, which we were forced to keep secret and then destroy, for fear of them falling into the hands of Admiral Marcus's associates. You were clinically dead for nearly twelve hours, Captain, and have been in a coma for over a month. Khan has been returned to cryo-storage, and Section 31 has been disbanded under Starfleet order, under the insistence of Admiral Barrett, who incidentally was also Captain Pike's former First Officer. There have been multiple changes in the chain of command while you have been…unconscious."

Kirk's eyes widen, though Spock is somewhat mystified at the lack of grief over the reminder of Captain Pike's death, not so long ago. "I…wait." He reaches up an unsteady hand, pinches his forehead. "You mean…Khan, as in, Khan Noonien Singh?"

McCoy pauses in the act of calibrating the cardio-oxygenation sensor, and slowly turns back toward the bed. "Jim," he says cautiously. "How much do you remember, from before you went into the warp core chamber?"

"The – oh, God." The captain's face has gone an alarming shade of white, and Spock steps forward in alarm. "Bones?"

"Jim, what is it? Y'need to calm down; whatever it is, you don't need to worry about it today, okay?"

"Bones, what year is it?"

Both of them stop, and stare in surprise at the apparently inapropos question. Kirk glances at the two of them, then around the room and back again, eyes flashing in what looks like increasing panic.

"What year is it!"

"2259, Jim," McCoy replies quietly.

Kirk turns even more pale.

"Doctor, something is wrong." Spock edges closer to the bed, because perhaps physical proximity will allow him the insight which he has not had from his former distance. Something has been…off, this entire conversation, something he cannot quite put his finger on.

"Ya think!"

"Captain, perhaps you should rest," Spock suggests, hoping that the non-threatening suggestion may calm the man enough to help them ascertain what precisely is the problem, be it psychological or mental or emotional – or a combination of the three.

"I – no, that – Spock, I…" Kirk trails off, swallows hard as if he is going to be physically ill. "I…"

"Sir?" He settles cautiously on the edge of the bed, because the man looks like he is on the verge of a panic attack. While the unfortunate occurrence would be justified, given past recent events, delaying it would be preferable, and so he reaches out slowly in an effort to offer physical contact. He knows Jim is a tactile human, and in truth he would not object to the reassurance himself, after the events of thirty-nine days ago. "Is there something –"

He startles, as suddenly his hand is practically snatched with what can only be desperation, and before he can realize what is happening his fingertips are being placed into a rough approximation of the kash-kau position, something Jim should know nothing of as he and Kirk have never shared a mind-fusion.

This would in itself be cause for shock and trepidation, justifiably so, for no human should ever enter a mind-meld of any magnitude without being made aware of its consequences, and no Vulcan should ever perform one without being prepared, as the consequences themselves can be disastrous should the minds not be compatible – but that is not why only a moment later he stumbles back from the bio-bed, reeling with what that only seconds-long, brief contact has imparted to him.

McCoy's alarmed exclamations, punctuated by a series of quite colorful Terran swear words, ring dully in his ears over the knowledge which for a moment blots out sound and sight, before the sensory overload returns to normality.

"What the hell was that!"

"Doctor, control yourself," he manages, through a tense jaw, and sees the man shake his head in apology.

"Sorry. Look, I just knocked him out with a mild dose of pentathol-C, he's not allergic to that and it won't keep him out for long, but that scared the devil out of me. What was that?"

Spock shakes his head, trying to reel his senses back under control. He had not been prepared for that.

"Here, sit down, you look like you've seen a ghost. Heard a ghost? I dunno, whatever that voodoo is, it did a number on you. You want I should give you something for the headache?"

"Negative, Doctor. I am quite all right."

"Then what in heaven's name even was that?"

"That, Doctor, was a rough approximation of a mind-meld, or mind-fusion – a Vulcan mind-joining. It is a highly intimate mental act which the captain should know nothing of, or at least should not know how to initiate, much less be able to do so with me, as I have never mind-melded with him. No human should be able to initiate such a mental channel without considerable practice in the act."

"That's…alarming." The doctor looks more than slightly frightened. "I have no idea if Khan had any telepathic abilities, but if he did, and they're comin' through that serum and being manifested like that, we have a major problem."

"I do not believe that to be the case."

"You…how can you know that?"

"I did not gather the impression, through the mind-meld, that the abilities were anything other than simply and innately human; I received no indication of any enhanced, superhuman qualities."

"Oooookay? So?"

"So, that is not the problem at hand, Doctor."

"What is it, then?"

Spock moves over toward the bed, but remains a safe distance from the man once more lying still and pale against the white sheets. He looks up to see McCoy watching him, posture tense with protective concern, and their eyes meet over the whirring med-scanner.

"The problem, Doctor…is that this man is not Captain Kirk. Or more accurately, not our Captain Kirk."