Disclaimer: Star Trek belongs to Gene Roddenberry. The new universe belongs to J.J. Abrams and Paramount.

A/N: So there have been rumors floating around about the new villain in the next Star Trek movie. has confirmed from several sources that Benedict Cumberbatch is playing Khan, but that the movie will not be a rehash of Space Seed or the Wrath of Khan. At first I was conflicted when I heard this – I really did want them to do something original. But I can't really blame them for wanting to have their own crack at Khan; if I were in their shoes I would be tempted to do so myself.

I have decided to write my own story about reboot Khan, Kirk, and Spock before I see the movie. I will be imagining Cumberbatch as Khan, and trying to explain worrisome details as to why the new Khan is white and not quite as buff as the old one. It will be, of course, set against the backdrop of Kirk and Spock's developing relationship. It's going to be a long fic, and hopefully I'll have it done before the movie is released next May. I hope you all enjoy the ride!

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This is AU and separate from the movie.

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The Return of Khan

Ch. 1: Discovery

.~.

U.S.S. Enterprise, 9 months into the five year mission

Kirk supposed it had all begun with the mind meld back on Delta Vega. Ambassador Spock had only meant to transfer information concerning the attack on Vulcan, but in light of the recent disaster, his control was not what it might have been. There were images that slipped through during the meld, images of a much younger Spock and his Kirk. Joined hands, a ceremony, parted from me and never parted… There was no doubt about it - his counterpart and the Spock of that time had been lovers. Not only that, but they had actually gotten married, or whatever the Vulcans called it.

Talk about having his mind blown! One couldn't blame Kirk for having doubts about his supposed destined epic friendship with Spock, as the Spock of his universe had been the one to banish him on the godforsaken planet in the first place. Still, after the earth was saved and the mission over, Kirk could now safely say that the Vulcan didn't hate him, that he might even respect him. After all, they'd made a pretty awesome team.

So it only made sense that when Jim had been given command of the Enterprise that he tried his best to convince Spock to be his first officer. To his utter disappointment, the Vulcan had declined, stating that it was only logical to help rebuild his race. Kirk understood that, wished him luck, and tried his best not to take Spock's rejection personally. By the time they were set to warp out, he hadn't chosen another first officer – hoping against all hope that Spock just might change his mind at the last second. And the amazing thing was, Spock did change his mind! The Vulcan appeared on the bridge just as Jim was giving the order to leave. That he was willing to leave his people to serve on Jim's ship brought out a surge of fondness in the captain. At last, with Spock's arrival, his crew felt complete.

Jim knew that even without the insight into his alternate future, he would've been drawn to Spock. The Vulcan absolutely fascinated him. There was much more to Spock than coldness and logic. He had a very subtle sense of humor, which only Jim seemed to catch. He was a brilliant scientist, and was a patient teacher to those who worked under him. And for a Vulcan, he was a bit of a rebel. He was the first Vulcan to choose Starfleet over the VSA, and against his father's wishes, too.

Jim had to work hard to befriend the Vulcan – apparently there was a big difference from respecting someone and actually wanting to hang out with them. It had taken months, but finally Spock was thawing out a little around him. He'd become more receptive to Jim's suggestions that they spend more of their leisure time together. It started with a chess game here, a sparring match there, until finally Jim and Spock were spending many of their off-duty hours together. It was, in Jim's book, a real win. If he couldn't be with Spock romantically, as he was currently dating Uhura, he could at least be one of his closest friends. Jim tried to squash his more-than-friendly feelings for his First way, way down, but they often surfaced at the most inconvenient of times.

But the universe was often cruel to Jim. Strangely, Spock started coming to Jim for advice concerning his floundering relationship with Lieutenant Uhura. Jim tried to convince the Vulcan that he really wasn't the right person for that job, but Spock paid him no heed. So Jim was stuck trying to help the Vulcan he really wanted to date salvage his relationship with someone else. Now, he wasn't about to try and steal Spock from his communications officer. One little mishap at the academy between Jim and another student who'd been in a relationship had made him feel both dirty and guilty. Needless to say, he was totally against breaking up couples for his own benefit. He wasn't completely without morals!

Jim liked Spock, he really did, but sometimes the Vulcan's emotional immaturity could really frustrate him. Whenever Spock was being especially difficult to get along with, Kirk imagined the look of absolute adoration on elder Spock's face when they'd first met. Jim would give anything to see that expression on his own Spock, even if it would take years for him to accept his emotions and proudly display them.

Jim remembered the last time he spoke with Spock's counterpart - right before they left on the five year mission - quite vividly. He had an affinity for the old guy, and held him in the highest respect. It was only logical that Jim treasured his advice. But when the ambassador had warned him of a 300 year-old ship called the SS Botany Bay, he had laughed. He quickly sobered up when he saw the pain in the old Vulcan's eyes. Without divulging too much information, Elder Spock had implied that one of the individuals on the ship had caused a great deal of heartache for both himself and the Kirk of his timeline. He'd made Jim promise that if the Enterprise ever came across that ship, they would not make contact with it for any reason. Kirk never thought that he would have to test that promise – until now.

While on a routine milk run, the Enterprise had come across a small sleeper ship adrift in space. Its design indicated that it was quite ancient, perhaps even manufactured during the Eugenics Wars. It was policy that whenever a starship encountered an unknown vessel, the crew must scan the ship for life signs, in case someone was in need of a rescue.

"Are you reading any life signs, Mr. Spock?" Kirk asked, knowing his first officer had begun his scans the moment the ship had been sighted.

"Affirmative, Captain," Spock responded. "They are faint, but there are no less than twenty-two life signs."

"Keptin, I don't understand what a ship of that age would be doing out here," Chekov noted.

"What indeed?" Kirk murmured. "Uhura, hail them."

"I've already tried, sir," she replied. "No response."

"Guess we'll just have to do this the hard way." Kirk cracked a smile. "We'll send a shuttle over to determine the state of the passengers before we can beam them aboard. The away team will consist of myself, Doctor McCoy, and three security officers. As a precaution, we'll all wear the air-tight bio suits, since we don't know exactly what awaits us over there."

"Captain, we're close enough to magnify the hull. Perhaps it will give us a clue as to what the ship is doing way out here," Sulu suggested.

"It can't hurt." Kirk shrugged. "Let's see it." Suddenly, huge block letters proclaiming SS Botany Bay flashed on the viewscreen. Kirk's mouth fell open in shock, but he quickly closed it. "On second thought, belay my order. We're getting out of here. Warp two, Mr. Sulu."

"Mr. Sulu, belay that order," Spock said sharply. "Captain, as your First Officer, I must disagree with your current plan of action. If there are life forms on board, it is our duty as Starfleet officers to aid them."

"I understand that, Mr. Spock, but I really need you to trust me on this one." Kirk's eyes pleaded at Spock, but the Vulcan ignored it.

"I cannot allow such a substantial breach of protocol unless you can offer a valid reason for it."

"Okay." Kirk smiled grimly as he rose out of his chair. "Sulu, hold here for now. Spock, in my ready room." The Vulcan followed him without question so they could discuss the matter in private.

"Have a seat," Kirk offered, gesturing toward the chair opposite his desk. After they were both seated, Kirk began.

"I get why you questioned me. If our positions had been reversed, I would have done exactly the same thing."

"Captain?" Spock questioned.

"It's Jim, Spock," Kirk said, exasperated. "How many times must I ask you to call me Jim?"

"I do not know, Captain."

Kirk just shook his head. One day, he would wear his First down. "Look, I know I should have told you about all this before, but since I thought the odds of it happening were astronomical, I thought, why bother?"

"Explain," Spock said crisply.

Kirk winced. "Before we left, I had a talk with the other you. After wishing me good luck on my voyage, he made me promise that if we ever came across the SS Botany Bay, that we would not make contact with it."

"May I ask why?"

"He didn't go into a lot of detail – I guess he didn't want me to know too much about my possible future. But he did say that someone on that ship did something that really hurt him and his Kirk."

"I see," said Spock, raising an eyebrow. "Did he happen to mention a name?"

"No."

"That is regrettable."

"Now do you understand why I did what I did?" Kirk asked.

Spock raised an eyebrow. "Not precisely. Our future has been altered, thanks to Nero's interference. There is no reason why someone on that ship would act in the same manner towards us, as they did in a different timeline."

"Maybe," Kirk considered. "But you weren't there when I was talking with other Spock. You didn't see the raw pain on his face, in his eyes. Whatever that person did, they must have really screwed him over."

"Perhaps you should contact my counterpart," the Vulcan suggested. "I cannot make an informed decision on this matter if I do not have all the facts."

That sentence was just so Spock that Kirk had to bite back a grin. "Alright, we can try, but I don't know if he'll want to talk about the specifics," the captain cautioned. Kirk activated the video chat controls on his computer, and entered the frequency for New Vulcan. Thankfully, it didn't take long to make contact. A young female Vulcan appeared on the screen.

"Greetings. I am T'Sira, aide to Ambassador Selek."

"Hi, this is Captain Kirk and Commander Spock on the Enterprise. We really need to speak with the ambassador."

The Vulcan slightly tilted her head and responded, "that will not be possible; the ambassador has meetings for the duration of the day."

"You don't understand," Kirk pressed. "This is really important! He'll want to talk to me, I promise you that."

"It is urgent," Spock added, when T'Sira looked to him for confirmation.

But the aide would not budge. "Captain Kirk, I will inform the ambassador that you called. He will return your call at his earliest convenience."

"Fine," Kirk spat. "Tell him that the scenario he warned me about – it just happened." He severed the connection and then looked at Spock, as if to say 'what next'?

"Captain, we are obligated to investigate that ship."

"I know." Kirk's brow furrowed as he weighed his options. "We could hold here until the ambassador gets back to us. Then we'll know what we're up against and we'll know what to expect over there." Somehow he didn't think Spock would go for that, but it was worth a try.

"The life signs that registered were very faint," Spock reminded him. "Those aboard may be ill or dying. Any time we waste waiting could prove to be fatal to them."

"I know, I know!" Kirk took a few seconds to compose himself. This wasn't Spock's fault, and it wouldn't help matters if he got upset. Sometimes he would kill for that Vulcan control on his emotions. "I just don't want to get someone from our crew killed because I didn't take Elder Spock's threat seriously."

Spock just stared at him. "Captain, I doubt that a single being would be able of causing that much damaged to an armed security detail."

"Yeah, well," Kirk snorted, "I don't want to underestimate this possible threat."

"But you do understand the reason why we cannot just wait around."

"I do." Kirk steeled himself as he prepared to take action. "Okay, here's what I propose. We'll have an away team consisting of myself, Bones, and fifteen members of security. We'll all be equipped with the biohazard suits and phasers. At the first hint of trouble, we'll beam back immediately. The protective suits are a must, since who knows what kind of environment we'll find ourselves in. Is that to your satisfaction?"

"I must ask why I was not included in the away team."

Kirk inwardly cursed. He was really hoping that Spock wouldn't bring that up. Since he really couldn't say 'because I want to make sure you're safe,' he gave the standard answer about how it was against regulations for a captain and first officer to go on away missions together.

"I am aware of that regulation, however you have bent that rule eight times in the past," Spock reminded him. "Why will you not break it now?"

"Because I want to take every precaution that my ship and crew will be safe. I can't stress how serious Elder Selek was when he warned me about this ship. If something unforeseen happens to me, I'd want you to be able to immediately assume command." Please, please, please let him buy that, Kirk thought.

"Very well," his First relented, but made no move to leave the room. "Captain, may I offer a suggestion?"

"Go for it." Kirk braced himself for more complaints.

"Perhaps there is a member of the crew that minored in the study of the Eugenics Wars period. It may prove to be helpful when you meet the people on that ship."

"That's a great idea!" Kirk smiled warmly at the Vulcan, thrilled that he wasn't being reprimanded. He asked the computer to perform a search for just that, and was rewarded with the name Lt. Marla McGivers. "I'll definitely add her to the away team list."

"And procedure outlining the transfer of the crew of Botany Bay?"

Kirk tried not to sigh – he really wished the Vulcan would display a little more faith in him. But he knew Spock was only doing his job. "I will make sure Bones follows all of the necessary protocols before they are beamed over. I'm not taking any chances with these people."

"Very well, Captain. That is all."

Spock followed his commanding officer back on to the bridge, where he then took temporary command of the ship.

.~.

The away team beamed aboard the Botany Bay without any trouble. When they materialized, Kirk was immediately on his toes. He quickly scanned his new environment, phaser at the ready. While he didn't see any threats, he wasn't about to be lulled into false complacency. Even though he and his crew were all wearing the bulky biohazard suits, which protected them from almost all of the unknown elements, he was still worried. Ambassador Spock had issued that warning for a reason – he wasn't going to take it lightly.

"We all stay together – that's an order." Jim's voice crackled over the suit's voice unit. "I don't want anyone wandering off until we're sure these people are friendly."

A chorus of muffled 'yes sirs' followed.

"Doctor, scan for life signs," Kirk instructed.

"Jim, I have a readout of twenty-two life signs, which match up with the readings we took from the Enterprise," McCoy relayed after consulting his tricorder. "But, as before, they are extremely faint."

"Thank you, Doctor." Kirk nodded at his friend. McCoy was about to voice his curiosity as to the nature of such low readings, but when he noticed the pinched look on the captain's face, he wisely kept his mouth shut. He didn't want to add to the kid's stress.

"Captain, this ship is positively primitive in its design." McGivers sounded awed as they moved through the silent corridor. "I never thought my minor would come in handy in the field, but this is just-"

"Save it," Kirk snapped, whipping around to face the redhead. "Just help us search for survivors, and if you see something you recognize, speak up."

"Sorry, sir." McGivers sounded properly chastised.

Kirk felt bad for snapping, but he really didn't need anyone getting distracted. Whatever this threat was, he needed all of his hands to stay focused on locating all of the life forms. And the sooner the better – Kirk didn't want to admit it, but something about this ship gave him the creeps.

Just then, they all noticed a burst of white light about thirty yards in front of them. Jim sped up, bursting into a run as his crew flanked him from behind.

"By God, it's a sleeper ship!" McCoy exclaimed, as the recently illumined human body came into view.

Jim tried contained his surprise - this was not what he'd expected at all. He knew that the old sleeper ships allowed crews to enter hypersleep for the duration of their journey. They had been commonly used two centuries ago, before faster space travel rendered them obsolete. This meant that whoever this person was in front of them, he was likely over two hundred years old!

"That must be the captain," McGivers assessed as they came to a stop in front of the sleeping man, who was separated from them only by a glass barrier. The man was tall, with dark, curly hair and pasty white skin. "He would be awakened before the rest of the crew, upon arrival at their destination. I think our presence on the ship must have activated his sleeping unit."

"Bones, is he in good health?" Kirk asked, as they all watched the man's chest rise and fall.

"Seems to be," McCoy replied after waving his medical scanner along the length of the glass. "He's slowly coming out of hypersleep now. However I have no way of knowing if he carries any kind of pathogen, not until I get a reading on the air inside."

Without warning, a klaxon began to blare at the exact same time as the controls to the unit began to flash red. Jim watched, alarmed as the sleeping man experienced the symptoms of a heart attack.

"Subject is entering cardiac arrest," Bones confirmed, as the body began to shake erratically. "Permission to break the glass."

"Granted," Kirk allowed, watching as the doctor used his phaser to break a hole in the barrier. McCoy then pulled out his med-kit, found the hypo he needed, and administered it to the man.

"No effect, Captain! I request permission to beam him directly to Sickbay."

Kirk stood firm. "Denied – scan for pathogens first."

McCoy didn't waste any time giving his captain an incredulous look, although he most desperately wanted to. There had been other missions when he'd requested a beam back without taking all the regulatory precautions, usually to save someone's life. Before the beam back, he'd had Sickbay personnel erect a forcefield around the patient's bed, effectively quarantining them. With that precaution in place, the danger to others on the Enterprise was slim to none. Jim had never delayed him from carrying out this procedure. The doctor wondered why he was doing so now. That kid better have a damn good reason, McCoy thought to himself as he ran the safety scan. While the scan only took about forty-five seconds, that time could mean the difference between life and death in a heart attack victim. The doctor waited and watched, feeling helpless as the seconds crawled life.

"Scan is clear!" McCoy announced. "Permission to beam us directly to Sickbay."

Kirk hesitated for only a brief moment, before answering, "Granted."

A few seconds later, McCoy and the mystery man vanished. Kirk desperately hoped that by beaming the man over to his ship, he hadn't already set in motion the events that elder Spock had warned him about.

"Captain, should we try to activate any of the others?" McGivers asked, gesturing to the sleep unit next to her which held a blonde woman.

"No," Kirk decided, a little too quickly. "We, ah, wouldn't want to risk them going in to cardiac arrest without a doctor around."

"Very well, sir."

Kirk cleared his throat and addressed the group. "Alright, everyone. We're going to beam back."

"But we just got here," one of the security officers pointed out.

Kirk glared at him, and made a mental note to talk to the man about his insubordination. "I'm aware of that, Ensign. But as the survivors are going to be staying in stasis for now, there's nothing more to do here. We will tow their ship along with us, and after we have questioned her captain, we will develop a plan to safely bring each one out of hypersleep." Then, the captain activated his voice unit, and contacted his ship. "Enterprise, beam back the away team." He watched as his crew disappeared in groups of six. Finally, it was his turn to return to the ship.

Kirk had never been so relieved to see the familiar sight of the Enterprise's transporter chief. Now that he was safe back on his own ship, he couldn't wait to get out of the bulky suit.

.~.

The following day, in Sickbay

Dr. McCoy was treating Ensign Schmidt's minor burn with a dermal regenerator when he heard a groan.

"I'll be right back," he promised Schmidt as he rushed over to the bed that held the mystery man. The man was sitting up in bed, his flashing eyes coming to rest on the doctor.

"Where am I?" The man demanded in a low, silky voice. He seemed incredibly alert for someone just coming out of a 300 year sleep.

"You're on the starship Enterprise in the medical bay," McCoy informed him. "Please try to relax – we mean you no harm."

"Then why does my chest hurt?" The man asked, still suspicious.

"When we brought you out of hypersleep, you had a heart attack," said McCoy. "Fortunately, I was able to stabilize you. Other than that, you're in perfect health."

Some of the tension seeped out of the man's sculpted face. "Who are you?"

"I'm Doctor McCoy, Chief Medical Officer of this fine ship." He smiled tentatively at his patient. "I was hoping you would wake up soon – my staff and I have a lot of questions for you. How about we start with your name?"

The man's eyes darkened as he struggled to answer. What was my name? He thought, desperately trying to recall what it was. But it was no use. "I- I can't remember."

End Ch. 1

A/N: What do you guys think? Comments, questions, suggestions are always welcome, as well as constructive crit.