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A Light in the Darkness

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Summary: When the Eugenics War started, it wasn't just the Augments who were targeted. Now, it's time for vengeance. MAJOR SPOILERS FOR INTO DARKNESS

Categories Author Rating Chapters Words Recs Reviews Hits Published Updated Complete
Star Trek > Star Trek 2009 > Buffy-Centered
Star Trek > Other/General
KrysstiniaFR18519,616133911,25530 Jun 131 Jul 13Yes


Hello, all. I've got a new story! This idea came to me shortly after I first saw Into Darkness in May. I've been working on it since. This has major spoilers for the movie, so if you haven't seen the movie and don't want to be spoiled, you have been warned. A huge shoutout to by Beta, Forever Waiting for reading this over for me.

Star Trek and Buffy do not belong to me. I've written this for fun and am making no money.

I hope you all enjoy this and please leave feedback. I adore feedback!!


The first thing she saw was the bleach white ceiling that could only come from a hospital room. Buffy quickly took stock of her body. When she had agreed to be put in the cryotube, the ship had been under attack and it was unclear if any of them would make it. Obviously they had made it, but where were they and how long had they been floating in space?

The bruises and cuts she remembered having when she got in had completely healed. Her left arm had healed and her body was back in fighting condition. She slowly sat up, flexing her hands as she swung her legs over the side of he bed she was sitting in. “You’re awake, then? Nice to know you’ve survived, Summers.”

There was only one person Buffy knew that had that rich, baritone voice. “Khan,” she said, nodding slightly. “Do you know anything about where we are?”

Khan tilted his head to the right and pointed with his eyes to the corner of the room. What was quite obviously a camera was recording them. “Only what I was told when I awoke. They are called Starfleet. They found our ship a week ago. Our cryogenic tubes were beginning to malfunction. To save our lives, they woke us up. Everyone else is stable, and asleep.”

Buffy nodded and rubbed her eyes. There was a soft whoosh and a door opened on the wall opposite the two beds in the room. “Thank you for bringing her up to speed.” The man stood tall, hands behind his back at parade rest and feet shoulder width apart. He wore a look on his face that made Buffy cringe. Khan didn’t look any happier. “Welcome aboard the Defiant. My name is Admiral Marcus. You were Summers and Khan. Now you are John and Elizabeth Harrison. If you would come with me?”

Buffy glanced at Khan. His face was unreadable for those who didn’t know him, but she could read the distrust and discomfort there as if he had told it to her. She felt the same way. The admiral reminded her too much of Professor Walsh and she hadn’t known the guy for more than a minute. “Why are we here?” she said, not getting up.

“Your ship was drifting in space,” Marcus said. “It has been for 300 years at the very least. You are the remainder of what was recorded in Earth’s history as the Eugenics War. We are familiar with you and what you were trying to do while on Earth. You and Khan were genetically enhanced to be better than the human race, to be stronger, smarter, faster. That’s what I need. I need you to help the Federation become better.”

“What about the rest of our people?” Khan asked.

“What about them?” Marcus said. “They will remain in Federation custody until I get what I want.”

“You’re holding them hostage,” Buffy surmised.

The admiral nodded. “If you do what I tell you, they will be safe. No harm will come to them.”

Buffy glanced at Khan again. She knew him well and she could trust him. She sent him a tiny nod. Khan turned his attention to Marcus. “What do you need us to do?”


Marcus led Khan and Buffy down the corridor and into the elevator. “Your aliases are married. You two will share living quarters on this ship until we reach Earth. When we arrive, I will take you to one of Starfleet’s top secret research facilities. There, I will explain to you what I need you to do. Until then, you are to remain in your quarters unless you are escorted by a crew member.” The doors to the lift opened and Marcus stepped out. Buffy and Khan followed. “Only the chief medical officer, my first officer and I know who you are; no one else on this ship knows your true identities. I’d like it to remain that way. Someone will be by three times a day to escort you to the mess hall for meals. We will reach Earth in about a week.” Marcus stopped by a door and put a code into the panel by it. The door opened with the same whoosh that the door in the hospital and lift had. “This is you. You should spend your time catching up on Earth technology. I’ll see you soon.”

Buffy and Khan stepped into the room. Buffy could hear Marcus locking it behind them, but choose to look around the room instead. The two of them were standing in the living area. A couch and two chairs, on either side of a coffee table, were positioned near the window that showed space. A machine was along the wall to Buffy’s left. Near the window, which ran along the entire back wall, and to Buffy’s left was another door that led to the bathroom. The bedroom door was in the center of the wall to Buffy’s right. On the coffee table were two PADDS that reminded Buffy of iPads, although these were transparent.

Khan went further into the room, exploring their surroundings and looking for any way out. She knew he would. He didn’t like cages and didn’t do well with authority. She didn’t blame him. She was much the same way and they both had too much experience with people in authority to trust Marcus at his word.

Buffy patted herself down and found what she was looking for, grateful that Marcus’s people had left her clothes alone. Both she and Khan were in the clothes they had been frozen in, and in a pocket of Buffy’s jacket, she found what she was looking for.
She took out a pen and the small pad of paper and wrote Khan a note. We are being monitored? Video, audio?

She walked over to him and placed a hand on his upper arm. He turned to face her and she put the note in his hand. He read it and nodded. He took her pen and added to her note. Yes, both. I bet they’ll have the computer monitor our access to their archives. We need to be careful.

Buffy nodded and put the pad and pen away. She sat down on the couch and picked up a PADD “Did Marcus tell you how to use these things? I have some history to catch up on.”


Buffy and Khan spent the week reading anything they could get their hands on and spent most of their time in their room. They only spoke to each other when they needed to ask the other a question about whatever they were reading at the time. By the time Marcus visited them again, when the ship had reached Earth, both Buffy and Khan were mostly caught up on what had happened in the 300 years since they had left Earth.

“Ready to go back home?” Marcus asked, rubbing his hands together.


The research facility that Marcus took them to was looking into a way to weaponize Starfleet. There were some great ideas, but the scientists didn’t know how to implement them. “What I want you to do,” Marcus said, when he introduced Buffy and Khan to Agent Stiles, head of Section 31, “is to find a way to make all their ideas work. I want a starship that is a military marvel. It needs to go faster, be able to take on more damage, and be able to run on fewer personnel than the ships we have today. I want a working prototype in ten years. You two will make that possible.”

“What will we get if we do what you want?” Khan asked, keeping his voice as unemotional as he could.

“You will get your crew, in the end. Right now, you two will be able to work together. Stop cooperating with me and you’ll be separated. If you continue to be uncooperative, I’ll kill one of you. Maybe that will keep the other from making the wrong choices.”


“When will you awaken someone else?” Buffy asked. She and Khan had been working with Section 31 for a year. She had worked on ways to man a ship with the least amount of people possible and had narrowed it down to one, with maximum efficiency with two. Khan had developed plans to make the ship more powerful and stronger with a minimum increase in cost production. Everything that they had done so far was theoretical, but they were both fulfilling their end of the bargain, but Marcus had yet to fulfill any part of his.

“I need you and John to do a keep cover mission for me.” Marcus ignored Buffy’s demand and continued on what he was originally there for. Khan abandoned his research station and made his way over to them. “John,” Marcus nodded to him. “I have a mission for you and your wife. It is specially suited for people of your talents and I think you’ll enjoy it.”

Buffy inwardly groaned. Lately, whenever Marcus said that, he was planning to run them through their paces, measuring their reflexes, strengths and endurance. Khan’s face, as ever, was expressionless. She managed to keep her face expressionless as well.

“Your mission is to infiltrate Klingon space. We need full technical readouts of their spaceships, especially their tactical, navigational, and engineering systems. Get the information any way you can and get back to Federation space. Your ship is waiting for you. If you don’t come back within six months, I’ll kill one of your crew at random for each week you’re late.”

Khan’s eyes narrowed angrily, but he nodded. Buffy, following his lead, nodded as well.

“Good luck, then, John, Elizabeth. Come back in one piece.”


Khan put the shuttle on autopilot and turned to face Buffy. “I’ve disabled any equipment they could be using to spy on us.”
Buffy relaxed and exhaled deeply. “Thank god.” She slumped in her chair. For the past year, they were under constant observation and the feeling of living in a fish bowl was one she didn’t enjoy. Khan was the only one who kept her sane and she would wager she had done the same to him. “What are we going to do?”

“There’s only one option at the moment,” Khan said, rubbing his face with his hands. “We must continue to cooperate. There is a slim chance that one can get away without the other…”

“I’m not leaving you to the likes of Marcus, and you’re not leaving me,” Buffy interrupted.

“But would be easier if we escaped together,” Khan continued. “Those people aren’t just my people, they’re yours too.”

Buffy nodded. Willow was one of the frozen. Xander, Faith, Giles, Rhona, Vi, Kennedy, and any Slayer that had survived the Purge was there, bringing the total frozen to 144, that had survived. When the Augments had been targeted, Earth targeted anyone who was more than human, whether they be their own science experiment that had gotten away from them, or the ones that had protected them from monsters. Slayers had been grouped in the same category as the Augments. Buffy and Khan approached each other and formed a pact to ensure their survival and had been kicked off the planet at the end of the War. History said that the Augments had been trying to take over the world. Buffy and Khan were just trying to save their people from extermination.

“We have to continue to play the Admiral’s game and wait for the best opportunity.”

Buffy nodded, and grabbed Khan’s hand. “I’m glad you’re here with me. I would’ve broken years ago if you hadn’t helped me keep strong.”

Khan pulled her close and held her tight. “I know. You have made this more bearable. I can’t tell you how grateful I am that you agreed to join forces all those years ago.”

Khan pulled back slightly and kissed her. The kiss was passionate and heated. She kissed him back as furiously as he kissed her. Khan picked her up and carried her to the back of the shuttle and laid her on her back on the bench seat. Qu’noS was several hours away at maximum warp, they had plenty of time.


Seven years after their data collection mission, Khan and Buffy were still the only members of their sleeper ship that had been awoken. The two of them were working on special torpedoes when Admiral Marcus approached them for another special mission. “We are under attack by a Romulan ship from an alternate future. You two must come up with a way to get the weapons you’ve been working on operational!”

“That’s impossible, sir,” Khan said quietly but firmly. “The power supply for the phasers isn’t yet calibrated and there is no ammunition. The advanced phasers aren’t ready.”

“The torpedoes aren’t ready either,” Buffy said, before the admiral could say anything. “We’ve barely got the materials together and are still waiting on some of the advanced pieces.”

“Is anything ready?” Marcus shouted.

“Not at this time. We didn’t have any notice that there was an attack,” Khan said.

As Admiral Marcus stormed away, Buffy smirked at Khan, who also had a satisfied grin on his face. “Set your tricorder to record the battle above. We might be able to use any data later.”

Buffy nodded. Some of their ideas had been put on the Enterprise during its most recent refit on Marcus’s orders as a test run. He was satisfied with their work so far, but not enough to awaken anyone else. She squeezed Khan’s wrist and went back to work, a different kind of smile on her face.


A year later, Khan came back to his shared quarters with Buffy with a big grin on his face. The ship they had been working on, christened the USS Vengeance by Admiral Marcus, was a few days from completion. Their crew was safely hidden in the torpedoes that they had designed a few years ago. Marcus was gearing up to start his war with the Klingons. It was time to get their revenge, save their crew, and make their escape.

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