Light in Darkness

Summary: Sequel to Coming out of Darkness. The time for the Enterprise and her crew's 5-year mission has finally come. The connection between Jim and Khan has grown, but Jim still has his secrets. How many of them will come to light during their mission? More importantly, how will he handle it when they do?

A/N: Warning…there will be BDSM starting in chapter 2 between Khan/Kirk, the reason for which will be explained when it happens. It IS mild so even those that aren't fond of it should be able to handle it…I hope. Also in later chapters there will be mentions of childhood trauma and other unpleasant things…though I won't go into as much detail as I am in some of my other stories.

Chapter 1

It had been a year since the events of what the media had dubbed 'The Marcus Tragedy' and Jim had no idea who came up with the names for these things. The truth had come out after Khan's trial and the public viewed him as another victim of Marcus' greed and manipulations. Starfleet had made him Jim's responsibility, and ordered to shadow Jim indefinitely…not that Khan ever complained about that order. Jim and Spock had taken him to New Vulcan to spend some time with their mind healers. It took two months before the healers decided Khan was no longer a ticking time bomb, Jim's words not the Vulcan's, and sent him back to Earth with Jim. After that it was up to Jim and his crew to help Khan integrate with society…a job that had nearly given Jim a panic attack at first. Khan had shown Jim nothing but kindness from the start, and after New Vulcan Khan had started to subtly seduce Jim…and still was really because Jim was conflicted. He was attracted to Khan…there was no denying that one…but at the same time he still remembered what happened to Pike. Now he was lying in bed and staring at the ceiling, his mind whirling with thoughts of their new mission that would hopefully start soon.

For his part Khan was patient. He was frustrated by Jim's hesitant wariness, make no doubt of that, but he was patient and Jim was worth it in his mind. He had spent a year becoming Jim's friend and earning his trust. However, whenever he asked why broken bones made Jim flinch…among other things…the blonde would shut down or change the subject immediately. Khan had submitted a long list of ideas for upgrading the Enterprise to make her more efficient and much safer from her enemies. Jim had been more than happy to implement them into the redesign, something that made Khan smile softly when he thought of it. He enjoyed designing things for the ship and her crew, especially things that would make them all safer. He was sitting in an armchair, reading up and refreshing his knowledge of the various races within the federation.

*Beep…Beep…Beep…*

Jim groaned and rolled over, forgetting he was at the edge of the bed, and hit the floor with a loud thump. A low chuckle of amusement reaches his ears from the living room as Khan heads for the door of their shared apartment. He stood with a wide grin as his command crew filed in, heading in to greet them until Uhura and Chekov started giggling at him. He looked down and realized he was only wearing his golden boxers, a light blush staining his cheeks before laughing it off. He struts past the bedroom door and over to his closet to get some real clothes on. Khan shakes his head with a soft chuckle as everyone picks a spot in the room to sit. Uhura, Spock, and McCoy choose the sofa with Uhura in the middle while Chekov and Sulu took the loveseat. Scotty and Khan each took an armchair, Khan lounging in his like a king surveying his kingdom. When Jim came out of the bedroom in skintight jeans and light gold t-shirt he looked at the seating arrangements and grinned widely.

"So…What's happening with our girl?"

Jim planted himself on the floor between Khan's legs, his head leaning back against the front of the chair while long fingers card through his hair making him nearly purr from the feeling.

"Cap'n, Warp Core has been fully upgraded to Khan's specs and may I just say…she's purrin' like a big jungle cat."

Scotty looked over at Spock as the Vulcan opened his mouth, his look just daring the Vulcan to comment on his wording. Spock closed his mouth and raised an eyebrow, causing a round of soft laughter.

"Excellent…Nyota?"

Nyota Uhura gave Jim a playful glare for using her first name, which only earned her one of his innocent grins that always made her smile despite herself.

"Comms. Have all been upgraded with an expanded range, and have had an auto-detect feature added for Romulan and Klingon transmissions."

The pleased look on her face gave Khan a sense of pride. Chekov pipes up before Jim can even turn to ask him for his report, causing a few soft chuckles at his eagerness.

"Nawigations has been updated as vell. Ze sensors now hawe a much vider range and can pick out ze possible threats more easily."

Jim grinned at him and ruffled his hair a bit. Chekov was like a little brother to most of them, especially to Jim. He glances at Sulu, who has now pulled the little Russian closer to his side, and receives a curt nod and a few short words.

"There were a few minor upgrades for the piloting console as well Captain."

Jim nods back and turns to his best friend with a bright grin on his face.

"Bones…your turn."

The doctor shook his head with a soft sigh, more than used to Jim's personality by this point.

"Medical Bay got some new equipment, nothing overly special. I also got permission to keep that Tribble on board since Khan's blood somehow made it sterile…thank god, don't need those things taking over the ship…Jim…no…don't look at me like that…"

Jim had looked up at Bones with his best kicked-puppy face…a look that almost always got him his way. Bones growled softly and Jim knew he'd won yet again.

"God Damnit Jim! Fine…you can keep the damned fur ball just stop looking at me like that."

Jim grinned in triumph while Bones grumbled in fond irritation. The rest of the group just smiled softly and shook their heads. Jim turned to his first officer and nodded.

"Spock…your report?"

"The equipment in the science labs has received significant upgrades, as have the sensor arrays on the bridge. Dr. Marcus was unable to join us as she is overseeing the final tests of the new weapons systems. Providing there are no unforeseen complications the Enterprise should be able to leave in three days time. Our first stop is to be New Vulcan to deliver much-needed supplies and a certain Ambassador we are both familiar with."

Jim's face suddenly breaks out into an ear-splitting grin that seems to infect the whole room.

"Awesome. I was hoping we might get the mission to take him back."

Jim looked up at Khan and noticed his confusion, giving him a soft smile for a moment. He quickly explains some of the unpublished details from the Narada Incident, and again he really wanted to know who came up with the names for these things. The look that came over Khan's face as Jim told him there was a second Spock in their timeline now sent Jim into a fit of giggles. Khan scowled softly at him, but the fondness in his eyes ruined the effect and made Uhura and Chekov sigh softly.

Three days later found the Enterprise preparing to leave the spacedock and head out on Starfleet's first ever 5-year mission. Scotty was down in Engineering and reported all systems ready to go, the rest of the bridge crew following suit as Jim stepped out of the turbolift.

"Keptin on ze bridge."

Jim grinned at Chekov as he lounged in his chair, Khan coming to stand behind him and place his hands on the blonde's shoulders.

"Sulu, set course for New Vulcan and take us out."

"Aye Captain."

Sulu did exactly that and they were soon at warp and heading to their first destination. Once they were moving the Elder Spock came to the bridge and started talking softly with Jim and Khan.

"I am quite pleased that the situation with Khan has turned out so well in this timeline…in mine things ended rather badly…though I cannot go into detail of course."

Jim snorted softly and shook his head.

"Of course not…Oh…did I tell you about my new pet?"

A handful of groans and a few giggles sound out around them at his words. The elder Spock merely smiled and shook his head.

"No Jim…I do not believe you have."

"I call her my 'Super Tribble'. Bones had injected a dead Tribble with a bit of Khan's blood which brought her back to life and somehow rendered her sterile…thank god right? Don't need an army of super-healing Tribbles taking over the ship…anyway she heals really fast now and has a really warm body temperature…much like Khan really…only she has fur and is more portable."

Khan scowled at Jim for comparing him to a Tribble before turning a dark glare on the rest of the bridge, daring them to make a comment. No one seemed to be bold enough to take him up on that silent dare.

"Fascinating."

Khan's glare turned to the elder Spock, receiving only a serene smile in return before the Vulcan took his leave and left the bridge…Jim's amused laughter following him into the turbolift and lightening everyone's spirits.

A/N: So here you have the introduction of Jim's new Super Tribble…I couldn't resist really. I had to make her sterile though b/c god forbid it breeds . lol. That leads to an important fact that hasn't quite occurred to Jim yet though. Bones knows but is worried about Jim's reaction…Khan suspects but won't say anything until he's sure. *evil grin*