Coming out of Darkness

Summary: During the events with Khan and Admiral Marcus Kirk forges a friendship with Khan. When Uhura yells at Spock that Khan may be the only way to save him he surrenders, in return Jim speaks on his behalf at his trial and Khan is released…with a few conditions. Starts on Cronos.

Warnings: Spoilers for Into Darkness. Slash, M/M, etc…if you've read any of my other fics this should not be a shock ^.^ Also…I sadly own nothing but my idea…I'm just borrowing the wonderful characters.

A/N: I saw the movie and my mind immediately brought out this idea which refused to rest…so here it is. I'm uploading the whole thing at once too.

Chapter 1

Cronos, the Klingon's home planet and the worst possible place for any member of Starfleet to end up. So why was Jim there watching Uhura being lifted off the ground by her throat? He growled softly, ready to run to her aid when a beam of light took out the Klingon holding her. Chaos promptly ensued as he and Spock lead the security officers out into the fight. He cursed violently when the two security men fell to the Klingons, but he had little time for concern as a group of the violent bastards was on him. One was about to crush his skull when another flash of light had the Klingons on the ground. He barely locked onto a pair of impossibly dark eyes before Uhura and Spock were dragging him behind some stone rubble for protection. Jim watched as the man they were after finished taking out an entire squadron of Klingons by himself.

"What the hell did they feed that guy?"

Uhura's half amused and half exasperated look made him grin slightly before their quarry stepped closer, blasting Spock's phaser rifle out of his hand like it was a toy. Jim wasn't sure of the man's motives but he was fairly certain if he had wanted them dead he wouldn't have saved them from the Klingons in the first place. The man asked how many missiles they had, and when Spock told him he simply surrendered. Jim stood to look him in the eye and accept his surrender, before punching him in the face repeatedly until he could no longer lift his arms.

"Captain!"

Uhura's cry caused a spark of something to appear in the man's eyes as he whispered the same word, sending an involuntary shiver through Jim before he told Spock to cuff him. Once they had him aboard the ship and safely contained in a cell in the brig Jim had Bones take a blood sample to find out what the hell made him so powerful. Harrison was surprisingly cooperative, and entirely too perceptive when he figured out that they weren't moving because of a warp core malfunction. When the man spoke as he and Spock were leaving he ignored Spock's warning, sending him back to the bridge, and returned to speak to his prisoner again.

"I watched you murder innocent men and women! I was authorized to end you…and the only reason you are still alive is because I am allowing it. So shut your mouth."

Harrison regarded the Captain silently for a moment before speaking, his rich baritone voice seeming to fill the space around them.

"I surrendered to you because, despite your attempts to convince me otherwise, you seem to have a conscience. I would have no chance to convince you of the truth otherwise. 2-3, 1-7, 4-6, 1-1. Coordinates not far from Earth. If you wish to know why I did what I did, go and take a look."

"Give me one reason why I should listen to you."

The Captain was glaring harshly at him and, as he tried to figure out why, something he had said back on Cronos clicked into place and he knew.

"I can give you 72...and they're here on your ship. I suggest you open one up."

Harrison paused a moment to let that sink in before speaking in a softer tone.

"Tell me something Captain…You mentioned a name when you accepted my surrender…a man named Pike. Who was he to you?"

He watched the younger man's glare soften with sorrow before he looked away.

"He was my mentor, my friend, and one of the best damned men I have ever known in my life."

As Jim turned to walk away he nearly missed the soft look of guilt that settled on Harrison's face…nearly.

He called Scotty, hoping that he'd check out the coordinates despite having resigned b/c Jim was an idiot…again.

Upon reaching the bridge he informed Bones and Spock of his plan to open one of the torpedoes.

"Are you outta your corn-fed mind? You're not actually gonna listen to this guy? He killed Pike, he almost killed you. Now you think it's a good idea to pop open a torpedo because he dared you to."

"Why did he save our lives Bones?"

"The Doctor does have a point Captain."

"Don't agree with me Spock, it makes me very uncomfortable."

Jim listened to Bones and Spock go back and forth a bit before intervening.

"Look we're gonna open up a torpedo the question is how."

"But Jim, without Mr. Scott onboard who exactly is qualified to just pop open a four ton stick of dynamite?"

Jim grinned and almost let out a laugh before Spock spoke up.

"The Admiral's daughter appeared to have interest in the torpedoes and she is a weapons specialist. Perhaps she could be of some use."

Jim turned to give his First Officer a confused look.

"What Admiral's daughter?"

"Carol Marcus. Your new science officer concealed her identity to board the ship."

Jim's face took on an amused yet slightly confused look at the same time.

"When were you gonna tell me that?"

"When it became relevant…as it just did."

Jim let out an exasperated sound before comming the aforementioned woman and asking her to meet with him. After speaking with her he decided to send Bones with her to take a shuttle to a nearby planetoid to open up a missile.

"You know, when I dreamed about being stuck on a deserted planet with a gorgeous woman there was no torpedo."

"Dr. McCoy may I remind you, you are not there to flirt."

"So how can these legendary hands help you Dr. Marcus?"

"Bones."

Clearly Jim's warning was ignored as Bones tried to impress the woman with a story about delivering Gorn Octuplets. Jim and Sulu shared an amused look before Jim nearly had a heart attack from the missile arming itself, Carol barely managing to stop it in time. What he saw when they brought it back sent his mind reeling and had him racing back to the brig, Spock right on his heels. He stood close to the glass and refused to flinch or step back when Harrison pressed himself closer to the glass between them.

"Something I can help you with…Captain?"

Jim suppressed a shiver and stared blankly at the man as he tried to suppress his confusion and curiosity.

"Why is there a man in that torpedo?"

"There are men and women in all those torpedoes Captain…I put them there."

"Who the hell are you?"

Harrison gave Jim a an odd look before answering slowly.

"A remnant of a time long past…genetically engineered to be superior so as to lead others to peace in a world at war. We were condemned as criminals and forced into exile. For centuries we slept, hoping that when we awoke things would be different…better. As a result of the destruction of Vulcan your Starfleet began to aggressively search distant quadrants of space. My ship was found adrift, I alone was revived."

"I looked up John Harrison. Until a year ago he didn't exist."

"John Harrison was a fiction, created the moment I was awoken by your Admiral Marcus to help him advance his cause. A smoke-screen to conceal my true identity. My name…is Khan."

The look Harrison gave him was one Jim was unsure how to interpret, could only name as intense.

"Why would a Starfleet Admiral ask a 300 year old frozen man for help?"

Khan gave Jim an amused smirk at his sarcasm, liking the bold young Captain more and more.

"Because I am better."

"At what?"

"Everything."

Jim felt Khan's low voice, felt the hidden danger and power in it, flowing over his senses like silk. Khan could see the reactions Jim was trying to hide from him and it only made him more interested in the younger male.

"Alexander Marcus needed to respond to an uncivilized threat in a civilized time, and for that he needed a warrior's mind…my mind…to design weapons and warships."

"You are suggesting that Admiral Marcus violated the very regulations he vowed to uphold simply because he wanted to exploit your intellect?"

Jim sighed softly and let his forehead thunk softly against the glass, trying to decide if Spock would hit him for laughing at his naivety about human behavior. Khan spared Jim a momentary glance filled with understanding before hissing at Spock in a dangerous tone.

"He wanted to exploit my savagery. Intellect alone is useless in a fight Mr. Spock. You can't even break a rule, how would you be expected to break bone?"

Khan noticed Jim's flinch at his words and resolved to find out later why he seemed to have a problem with that part of his little speech over any other.

"Marcus used me to design weapons to help him realize his vision of a militarized Starfleet. He sent you to use those weapons…to fire my torpedoes at an unsuspecting planet…and then he purposely crippled your ship in enemy space leading to one inevitable outcome. The Klingons would come looking for whomever was responsible, and you would have no chance of escape. Marcus would finally have the war he always talked about, the war he always wanted."

"No."

The harsh whisper from Jim made Khan frown at him.

"No. I watched you open fire on a room of unarmed Starfleet officers. You killed them in cold blood."

"Marcus took my crew from me."

Khan turned away from the other two men so they would not see the guilt and regret on his face at seeing the pain his attack had caused Jim…though he still heard it in the man's harsh and broken voice yelling at him.

"You are a murderer!"

"He used my friends to control me! I tried to smuggle them to safety by concealing them in the very weapons I had designed…but I was discovered. I had no choice but to escape alone. When I did I had every reason to suspect that Marcus had killed every single one of the people I hold most dear. So I responded in kind."

Khan turned to face them as a single tear made its way down his cheek and his voice softened. He watched Jim's harshness soften as understanding swept through him.

"My crew is my family. Is there anything you would not do for your family?"

Jim sighed softly. He could understand the man's reasons, he could, but he wasn't sure he could ever really forgive him for the loss of his mentor. He was about to speak only to be interrupted by Sulu comming him.

"Sir, proximity alert. There's a ship at warp heading right for us."

"Klingons?"

Khan shook his head at Jim for his question.

"At warp? No Jim. We both know who it is."

Sulu's reply confirmed that it wasn't coming from Cronos and Jim cursed fluently in several languages, making Khan and Spock both raise an eyebrow as they glanced at each other.