Author's Note: Nothing of this belongs to me expect the OC's I place in here. Everything in here in purely a Fan-Fiction from my own imagination. I will always take feedback and advice if you wish to give it and I will always take the advice into consideration. I have not watched the original show in a very long time so I apologies if something is wrong somewhere along the storyline. Even though I will likely be doing as much research as I possibly can do. However, this Fiction is based on the movie made in 2013, not the one from 1982. This is a John Harrison (A.K.A. Khan)/ OC.

Pronunciation of Kya = KY - ya

6/18/19

Chapter 1

Section 31 - 2258

"Have you found anything Doctor?" The Admiral asked curiously.

They'd never heard of anything like this before. At least not with the Human species. This was rather interesting. The ship had been found adrift then reported to the High command of Admiral Alexander Marcus.

"I'm not sure Admiral Marcus. These people, these… Beings are not entirely human. At least not like the humans that are born to natural causes. These Pods are not new." The Doctor clarified.

"What do you mean Doctor… Come on, don't be shy. I need answers!" Marcus growled. The delays to awaken one was truly becoming irritating.

"Marcus, these humanoid beings should not have survived this long in those Pods. Their possibly three hundred years old… If not older." The Doctor clarified.

Marcus wanted to know these beings as well. But he knew if Jasper continued to stale that he'd be forced to have someone else do it for him. Or do it himself, because if the Doctor was insinuating that these beings were different all because they shouldn't have survived in these pods for as long as they had Marcus definitely wanted to wake one up. "Well, then wake him up. NORRIS! Help the good Doctor Jasper would you." Marcus would have his way in the end.

Nurse Norris jumped with fright at the Admiral's shout for her, he was frightening. Admiral Marcus was definitely intimidating, no matter how much of an ass he was. Though, his daughter, Carol, was a peach, something she knew Carol had not gotten from her father. But Norris was not going to tell the Admiral that, least of all that she knew his daughter.

"Yes, Sir." Norris said, jumping into her orders and began assisting the Doctor as Marcus left. If they woke this being up, they could cause a lot of damage. Not only to the being but him to them. But his peaceful slumber had Norris captivated for some reason.

"Doctor Jasper? Are you sure we should be doing this?" Norris asked, nervous and very worried regarding this situation, anything can happen.

"Everything happens for a reason, Alice. Kya, I need some extra hands over here please." Doctor Jasper called over his shoulder to the Auburn-haired woman working on the Dialysis report of the beings' blood.

"Yes Doctor." Saving the report to finish for later, Kya rushed to aid the small team working on the individual.

"Alice, Kya. You both will stay here in the hospital and Lab for the night with me to observe his condition during this. But we need to try to keep him from Admiral Marcus as long as we can. I don't like the look in his eyes." Doctor Jasper softly informed them.

They had spent thirty minutes, carefully removing him from his Cryo-Pod, and the next twenty-four hours watching his vitals and condition as he slowly woke up. It was unbeknownst to them that they had been observed themselves from under their noses.

Section 31 Hospital Wing – Waking up

Khan has always been able to control the environment he was manipulating, always ten steps ahead. It was never selfishly done of course, but for his family, his people. Or was that something he had been telling himself for years or so to make him feel better about his emotions of rage against the humans for running them off and labeling his people War Criminals. The painful and terrifying memories of that fateful night they were forced to flee were still playing in his mind:

"KHAN! RUN!"

"MAGAL!"

He was forced to watch his friend and brother fall, his family was being hunted down and killed as they fled to the backup ship and their Pods.

"We can't help him, Khan! Come on, we have to go!" one of the others shouted, pulling him back towards their Pods ship. Hundreds of their people had been killed as it was. Their homes turned to ruin, the fire blazing the night's chilling winter air.

Their screams would haunt him for the rest of his life, and that of his mind while they slept. He only hoped they'd survive this. Helping those who were injured into their pods he then rushed to his own after launching their ship, he had been the last on board and the last to crawl into his Pod.

He had no idea he'd been awoken in a bright room, the white walls looked completely sterilized and even smelled as such. But the lights and the level of brightness stung his eyes he hadn't used in quite some time. Though, he wondered how long he'd been asleep. Things looked very different. More advanced, had they succeeded in finally finding a place or time they'd be welcomed in? He wasn't sure, and until he was sure, he possibly shouldn't wake many of them until they could find a home to colonize.

"Doctor, he's awake." He heard a woman's soft voice, she sounded worried, yet excited. His curiosity had gotten the better of him for a moment. Turning his head as slowly as he possibly could, his diamond blue eyes found a female with long waving Auburn hair pulled back into a tight hair tie. He was surprised to find she was a human, a thought that sent fear and anger through him. If the humans had found them, then maybe they weren't safe. A sudden rage of irregular beeps began on the monitor overhead, then suddenly changed. His vision became iris white with spots in his vision then began to blur, "Doctor, his heart rate is erratically increasing!"

"He's going into shock!" another woman shouted.

"Sir, Sir, can you hear me? I need to perform-" the Doctor tried talking to him, but Khan hadn't heard any more from the Doctor. His heart seemed to be failing him. How had this happened? He didn't know, his mind was moving so fast from the moment he'd woken up, then seeing the human had provoked his hatred, his anger, and his fear, his deep seeding sorrow from those he'd lost on their evacuation had aided in triggering his state which had resulted in him being sedated.

Three Months Later

Doctor Jasper was graced with a rather frantic call from his assistant upfront, regarding the Admiral and several armed people in the halls heading his way. This was ridicules, 'Doesn't he just has lovely timing. If only I could give him a piece of my mind.'

Marcus grinned as he swiftly walked into Jasper's office, his irritation had only grown with his old friend of thirty years after he'd left three months ago. He had done as Marcus had asked yet had continued to retain some information from the Admiral. Information Marcus had leached from their system. "Doctor Siv Jasper, how wonderful that you're here. Your assistant seems to have forgotten you and your team were currently in the building. She claimed you and the other Nurses were… "Out," and the Lab and Hospital were shut down until your return… Jasper did you truly think you could keep his mind from me… Now, show me this specimen of near perfection." Marcus demanded with a grin of power on his face.

Grinding his teeth Jasper took a breath of courage, "Perfection." Jasper corrected, nearly shivered at the sneering glare Marcus gave him.

Marcus had no idea what the Doctor was saying, but he was sure Siv Jasper had corrected his words, something he'd never really had done in years. "Excuse me?"

"He is not 'near perfection' Marcus. This being, his platelets multiply faster than I have ever seen. His healing is incredible. And his mind… That's a different topic altogether." Doctor Jasper wasn't sure why he was even telling this to Marcus. Probably because he knew deep down that all the man had to do was have his muscle heads for hire march in and force him to give them everything with a Phaser to his head, 'retire' himself and his enter staff and give the information and research to another team to finish. Doctor Jasper was not going to let his staff suffer from his desire to keep information from a mad man on a Chaos drive for War. Though he knew that eventually he'd be found sooner or later regarding having his files all automatically backed up to his drives at his home.

Alexander Marcus was not the man he had once known all those years ago. The spark of interest Siv Jasper saw in Marcus's eyes scared him all the more.

"Are you telling me that this… thing, is a genius humanoid being?" Marcus was filled with triumph and excitement at this. To have such brilliance on his side would do great for his goals. The Klingon's wouldn't stand a chance!

"He's genetically engineered Alex, what else would you expect?" Knowing he was still going to get glared at from his smart-ass remark, Siv took a deep breath to retain what courage he had left against Marcus, "Look at this," he said, handing Marcus the file he'd been putting together for his report the Admiral was going to see, either way, his confidence faltered for a moment when he realized that the file he had been making for Marcus was, in fact, still laying on his desk.

The file he'd handed Admiral Marcus was his personal file he had been gathering about the Patient over the many months they'd studied him while he slept and the last three months regarding the being's capacities to learn quickly and creativity from the graphs of ideas Khan had upon waking up. Options of healing, medical supplies and much more, along with home designs. But what caught the Admirals eye were the Weapons graphs Khan had allowed Siv to copy for the file. At this, Siv Jasper felt rather dim for even thinking this wouldn't have gotten to Admiral Marcus. Because now he had the specs.

The Doctor and his two Head Assistants had discovered Khan's art skills, which were impeccable, and his grasp of the new language pieced together the past three hundred years or so had been very well gathered, much more had also been discovered about him, from him and from the Historian they had brought in without the Admiral's approval, something he hoped they didn't find.

This male they'd woken up had barely spoken of his past, but he was slowly opening up, Khan was slowly beginning to trust them. Trust that Marcus was about to shatter in mere moment's once he finished looking over the file as he placed it under his arm with a grin. Jasper felt sick once he'd realized he'd basically just signed all his staff death warrant's by handing that file over. "Show me this man, this, Khan."

Jasper nodded as fear sank into his gut with unending knots as he walked the Admiral from the Hospital Wing and towards personal dorms. Siv hoped Norris's son wasn't with Khan. The six-year-old boy had found the man interesting. Siv Jasper's horrors became a reality upon opening Khan's Dorm room and found the kid with the unfrozen male. The smile that had been previously visible on Khan's face had been wiped from his face as the boy continued to admire the two gifts Khan had made the boy. A stuffed animal and a silver bracelet of some kind.

"Charlie, go find your mother, Doctor Jasper and I have a meeting I must have forgotten about. And remember what we talked about?" Khan spoke softly to the boy, setting him onto his little feet from his lap. The stern and stiff nature of the two men behind the Doctor told Khan pretty much everything he needed to know. The Doctor had warned him over the last few months of this man giving Khan three months to do plenty of research on him and much more. Khan was also under the impression his cooperation was likely going to be needed.

"Never go anywhere without them." Charlie repeated Khan's previous words to him a few minutes go.

"Good boy… Charlie, I actually have a better idea. Why don't you go and help with my project." Khan said to the now smiling boy. The idea had struck Khan in moments of realizing what was likely going to happen, and the boys' safety was one of his priorities. He was innocent in his young life and he had found Khan's work intriguing. Wanting to learn from what he knew as he did his work.

Charlie would watch Khan work on his projects or play hid and seek in his office, hiding in the hidden seat cabin against the wall of the small office the Doctor had graciously allowed him to use for his personal work through his recovery upon waking up. That had been three months ago. Khan's strength had fully returned to him, mind and body.

"Okay!" he said with excitement taking his stuffed squid and ran out the open door smiling with excitement.

"You gave him a room Doctor? These Dorms are for staff members… not Specimens."

"With all due respect Admiral Marcus, you left this small section under my care and guidance. He's been in a Cryo-Pod for three hundred years. I saw no issues with allowing him to roam around the dorm room sector. He has no access to the labs. He needs a key card to get in and out of the building or security key codes for the doors. I doubt he's going to run. You and I have very different ideas between a 'Specimen' and a Guest." The Doctor growled a bit, though his eyes had glared at the floor at the Admiral's black Starfleet boots instead of the man he wished to throttle. Siv had had enough, the Admiral was pushing it with him as it was, his outrages rudeness to the Male was outstanding.

"I can clearly see that, Doctor." Marcus glared daggers to his old friend. Marcus was careless as to the history he and Siv Jasper shared. Thirty years compared to now and the goals the Admiral desired so much was nothing to him now and what little heart he had left. To have this goal and the war he wanted between the Klingons and the Federation were outstanding, it also required many sacrifices. "Morva, have your team do a sweep of the sector and round up the good Doctors two head Assistance's." Marcus order.

The Man nodded and did as instructed, "And the kid?"

"Yes… Yes, unfortunately the kid as well." Marcus said with a regretful nod. He couldn't let this get out and unfortunately even with Doctor Jasper's small team on this. Marcus now had what he wanted he couldn't afford them tell anyone.

"They have a Historian here also, find him." Marcus ordered, gaining a nod from the man who relayed the information out to his team as the Admiral gave the Doctor a stern, disapproved look then over to Khan "Well, Doctor it seems you've been a busy man these last few months." Marcus said, his eyes never leaving Khan's.

"Alex, please don't do this-" "Oh, shut up Siv. Please, you're begging is useless."

A woman's loud screech was heard down the hall, "ALICE! YOU BASTARDS! GET YOUR FILTHY HANDS OFF ME! LET ME GO! SIV!" the woman screamed in increments of seconds after the first shot fired off.

At the Doctor's panic he rushed towards the door and the Admiral, an act he knew would likely set off the event's he was previously trying to avoid, "KYA!"

Morva quickly advanced the Doctor, slugging him hard against his jaw sending him across the floor to Khan's feet.

The Doctor knew he had failed in just about every aspect of trying to avoid any of this from happening. He was a Doctor, not a genius.

The Admiral was leaking his information from his lab either way, so there was truly nothing he would have been able to keep from Marcus for very long. Everything in the current file was everything he'd have found out eventually.

"What dignity Siv… I'd have thought you'd have been smarter…" Marcus said blankly to the fallen and painfully grunting Doctor as he turned his excited glance to Khan. "Now, I have some questions regarding your 'history'. Something I've actually found in the file right here in my hands. But first, I think we need to be clear on a few things before we leave. I don't see this place fit for active duty any longer." Marcus clarified with a smirking grin as he looked over to Kya, the shocked terror on her face was astonishing and boasted his ego quite a bit.

Jasper grunted as he looked up to the blank expression of the Augment, "I'm sorry Khan, I gave him the wrong file by accident… I'm so sorry."

'Typical really. He just killed his own team from his stupidity.'

"Shut up," Morva growled with an annoyed eye roll, shooting the Doctor in the head. The action had the male leaping into action, disarming Morva quickly and effectively. Though he had to admit the human had put up a good enough fight, for about ten seconds before Khan shot the man in the gut and aimed the weapon at the Admiral's chest. Khan would have been lying had he claimed he wasn't surprised the human Admiral didn't sheath away from him upon the fight breaking out. However, the dirty grin on his face was answered enough. Khan knew by his calm expression and the spark of interest and excitement flickering in the human's eyes meant that the Admiral had his hands on a couple of gambling chips that would no doubt require Khan's full cooperation. The first being the woman two of his hired gun's stumbled into the room with as she struggled against them, then there was the crying six-year-old, Charlie, in the female's arms. Each one holding a blank face.

Marcus cleared his throat as he rested his hands in front of him at an ease stance. His shoulders squared and head held high with demanding arrogance and power. Something that not only pissed Khan off but ignited his rage. He was using his own kind as hostages against the Human Augment, a lower species Khan knew he shouldn't have cared for. Yet the two in the room currently alive had wiggled their way under his harsh and cruel shield to safeguard himself. "Drop the weapon Khan, otherwise you're signing their deaths. And from the interaction between you and the boy I witnessed not too long ago, I'm going to go ahead and assume he has a close connection with you. Or are you really that heartless?"

This was a rather disappointing situation. Even if Khan killed every single one of the muscle heads in the room, the girl and Charlie would be killed in the process. The thought of their deaths was a bit uncomfortable to him, none of the humans, or other beings, in this small facility had desired to bring him any form of harm, nor the desire to exploit anything in his engineered nature. They had wanted to help him. Warned him against the Admiral. But Khan was cocky enough to believe his brilliant mind would be enough to save his people in the end if this happened. And it seemed things were just beginning.

Could he really save them both? Or did he only have enough time to save one… Khan hated to admit it, but if he were to save anyone in the room currently held hostage it would be the boy. He knew Kya would understand. And as he studied her eyes and expression, he knew she was expecting him to safeguard the boy.

"Khan… don't let them hurt him… please… Don't let them hurt Charlie… he's just a boy… he's done no wrong…" She begged.

Khan's suspicions were confirmed.

One of the hired guns growled at her outburst, slamming her harshly against the wall behind them causing her to scream and grunt in pain.

"Shut up!" he snarled at her. He was surprised when she had landed a solid punch to him, angering the man more. Slamming her back against the wall, the human backhanded Kya enough that the force had busted her lip, leaving a trail of blood down the corner of her mouth. The red mark from the impact began to form into a bruise.

She hadn't cried in terrifying pain, no, she had glared heatedly at the man who'd begun to us her a rag doll and punching bag with promises of dismemberment as a few tears slid down her face.

Khan's hands gripped the weapon with crushing force. He knew he heard the slight crack of the handle as he watched, his trigger finger itching to fire. "Are you truly willing to sacrifice yourself for the boy?" Khan wasn't sure why, but he had to know if she was bluffing him or if she was truly a victim in this just as any other who'd been attacked just moments ago. At that moment, Khan and Kya had shared a form of equality. The desire to save those they loved. His stomach tightened as he watched her tears roll from her bright coral blue eyes.

"…Yes…" Her heart clenched in her chest as she took a breath, of course, she was terrified. She was about to die and wouldn't have the chance to see her parents, wouldn't be able to see her dear cousin, Jim. She was so proud of him, even though she was the second youngest, her little brother being the real youngest of the family, she was still so very proud of him for his accomplishments. She heard the click of the Phaser that had likely been set to kill or Disintegrate as it was pointed at her neck. The sound of the click had caused her to flinch. Her eyes closing as a reaction of the fear. Her ears filling with Charlie screams, squirming as he cried.

It was like his family was being murdered all over again. The sudden realization that he'd just compared the two situations and clearly had the thought of family in his mind made him very uncomfortable. He hadn't minded seeing them as friends, but the thought of them possibly considered family at the back of his mind was a bit worrisome. But wasn't that the hope they had priory? To have comrades and alliances, then they'd been betrayed, and they were then the enemy. Their minds consumed with domination to lesser beings where they were superior in every way then they had to run. Betrayed by one of their own, a female, all because he had rejected her mating proposal. The memory was sour in his mouth, but the scene before him made him sick.

The Admiral was rather taken back with sheer surprise by the male's actions as he watched Khan drop the weapon, he'd disarmed from Morva and kicked it aside, his face clear of any form of expression, "You have my surrender and cooperation."

Grinning with victory, Marcus smirked. "Good, your Crew members have been moved to a safe location. Far from your hands. As of today, Mr. Khan, you are John Harrison. Kya, I'm placing you close so I can keep an eye on you. You are the only one here who has worked personally with Mr. Harrison and thus have firsthand knowledge of his anatomy if he gets hurt you can't be too careful and I'd rather much like to be prepared…"

"What about the kid, Admiral?" the woman said as the kid squirmed in her arms, an act that obviously didn't bother her. Khan made a mental note to find out if the woman had kids, or did she just not care whatsoever?

Sighing with a deep huff of uncertainty, Marcus rubbed his forehead as he thought, "Well, I'm not a child killer, I'd like to keep the kid quiet but-" Fear swarmed both Khan and Kya at the Admiral's words.

Her breathing hitched with fright. This was her breaking point. "He didn't see anything, Admiral, please! I'll take him, but please I'm begging you, don't hurt him!" Kya begged, struggling once more against the brute holding her, the second coming to help his team members hold her back.

For as small as she was the little thing had a nice swing, not to mention faster than they had imagined a Nurse Assistant to the Doctor to have been. Their only conclusion was that the woman clearly had to have training beforehand.

The Admiral seemed to consider letting her, but then again, the smallest person could get into tight places and out of them quicker, better and faster than someone of their adult size. The kid could be used to slip messages to another outside. His eyes drifted between Khan's stiff stance, his knuckles clinching in anger and grinned wickedly, "Put him in Mr. Harrison's Pod."

"Yes, sir." The female said blankly, turned and walked out with the screaming boy as the two men held onto the screaming woman as she fought against their hold, "NO! Khan! Do something! He won't survive in that thing! MARCUS PLEASE, DON'T DO THIS!"

"KYA! KHAAAN!" Charlie screamed down the halls, his voice became distant to them except to Khan's ears. A sense that was approximately four to six, if not more, times better than the humans.

"CHARLIE! MARCUS, PLEASE! DON'T DO THIS!"

Marcus groaned with a headache coming on from the woman's ear-shattering screams, "Oh for God's sake, shut her up will you- Do not shoot her! Or I put a round in your skull!" Marcus shouted, red in the face with anger when his man had held his Phaser to her head.

The fact that the Admiral hadn't wanted her killed, yet, was a bit surprising.

The scenes that played out, khan had been forced to allow to happen, his fists clenched tightly in a ball as his nails dug into the palms of his skin. How much he desired to rip them to shreds for this, but the sudden sound of metal meeting skull was a deafening sound to his ears as Kya dropped limply in the two men's arms now silent. A sight that lead him to believe she was dead, the emotion he was suddenly filled with stunned him more than almost anything in his life next to being betrayed all those years ago. His heart had slowed and felt as if it dropped to his stomach with his intestines knotting. However, he knew she was simply rendered unconscious but the constant chanting of that no his mind hadn't truly helped.

"Sorry kid." The woman said blankly to the boy as he cried into the stuffed Squid he cuddled to his face, a child's attempt to self-comfort as she placed in him into the Cryo-pod, closed the lid and activated it.

Charlie Norris was soon sound asleep in said Pod and escorted out over the limp bodies around the Hospital Wing of the small Lab under Section 31 along with the others and Admiral Marcus.

The small facility was permanently shut down, disbanded and cleared of any and all evidence anyone had been there.

Marcus proceeded to use the Pods and Kya against him. For reason unknown to Marcus Khan seemed to have an equally soft spot for the human woman and the boy. But he did his job diligently, and rather remarkably. Khan hadn't been harmed at all on the job, and if the occasion had occurred, he'd healed just as quickly with little thought it before Kya could get to him, leaving Marcus to decide to let her leave but continued to have reminders for her that she was being constantly watched with strict eyes.

Marcus had only allowed Khan one request, and that had been a request that truly stunned the Admiral, even Khan was struck by his own request. He had asked to take one of the many pictures from Alice Norris's office, a picture of Alice, a long-haired blond with bright blue eyes and Kya both holding a newborn baby Charlie. The picture had been taken in the park in the middle of summer. The two Nurses had told him they'd known each other for years threw medical school. Doctor Jasper had been their Professor at the time than their team Leader on the Project.

Though, as good of a Doctor as he had been, he wasn't exactly the best, nor brightest, when it came to contain information from someone, which had left them all in their current situation likely been the Doctor side of him when discussing a Patient.

*I hope you enjoyed the first chapter and I will gladly take Feedback. I know I didn't elaborate more on the details like I usually do, I apologies. I will likely go back to fix that but not until I actually see fit to, or when, and if, I think it needs the details added, however, I know the rest, unfortunately, going to be errors and corrections needed to be done, even though I try to avoid doing that I always seem to fail at it and find something that I need to fix. So, I will be coming back to fix errors along with chapter 2... Hopefully.

The first chapter is really more of a pre-dating informational chapter to how Khan, Kya, and the boy met as the story goes. Hopefully, this one turns out as good as the previous stories I have done, if not I still have the intention to finish it, no matter what.