Thank you for the lovely response to the first chapter, I hope this chapter doesn't disappoint. Bones is being a bad boy and telling lies to his Captain, Spock is skilfully getting on Kirk's nerves and Khan makes an appearance :) Please review and enjoy!

Chapter Two: San Francisco Bound:

It had taken forty-eight hours to reach Earth; during that time Jim remained in the Medical Bay to Bones's surprise; he also remained quiet as he contemplated facing Khan again. It was true, he had sent his request to Star Fleet concerning the man's removal from his cryogenic sleep, but actually knowing that it was happening and that it was happening because of something that was occurring to him made it seem so much more real; so very at the forefront of his mind. He was suddenly uncertain if he could deal with seeing the man again, the last time they had been face to face had been on board the Vengeance just after he had watched Marcus have his head crushed... It didn't make for an attractive memory.

Yet, at the same time, there were the better memories. While he, certainly, couldn't forget the terrible crimes Khan had committed he did feel a sense of kinsman-ship with him; the superhuman had obliterated the Klingons who had attacked them on Kronos; he had fed him information that he would otherwise never had had, and would likely have died without knowing; they had flown through space side by side in order to get to the Vengeance and Khan had saved him from being a pretty smear on the side of the large Star Ship.

There were so many things Khan had done right, so many things he had done properly and with consideration, they practically weight evenly against the things he had done wrong, the crimes he had committed. Maybe that was the problem, in being a superhuman Khan was able to subconsciously weigh up his actions so that regardless of them he could maintain a clear conscience?

Kirk shook his head, he couldn't afford to speculate about what went through the man's mind, he could never understand coldblooded murder, but he could understand the motivations of cold blooded murder. Well at least in Khan's case.

He looked up as he heard the usual mechanical clunking of the Enterprise docking at the space station above Earth; he stood up and straightened his uniform out before he looked around for Bones and saw the man tending to some minor burns.

"I'm going on ahead Bones, if Spock comes looking tell him I'll be at the shuttle." He called to the man, waving a hand lazily as he made a hasty exit of the Bay without waiting for a response from him.

He made his way off the ship and regretting it instantly, it felt like he was leaving home again; he shrugged the feeling off and made his way through the station, nodding and greeting a few members of the Federation and avoiding a couple of others as he made his way to the shuttle which would take them back to Earth, back to San Francisco. He briefly considered that if he had some time off he should head home to Iowa to visit his mother, but he then gave a moment of consideration to the fact that he really didn't want to spend any time with his waste of space step-dad, and quickly decided he would just give her a call instead.

Entering the shuttle and taking a seat at the front, closest to the pilot's cabin, and buckled the belts of the seat around his torso and waist. He rested his head back and closed his eyes; allowing his breathing to slow and his body to relax as he waited for the shuttle to fill up with the various members of his crew so that they could take off. He stiffened and jolted upright, his chest smacking off the belts around him as he had a sudden flash of frosted glass and a sensation of coldness rush over his skin.

Kirk glanced around, relieved when it appeared no one else had seen his miniature episode; he ran a hand through his hair and let out a long pent up breath, he shook his head and chuckled slightly at the stupidity of his 'moment' before he settled into his seat again as his Vulcan friend appeared out of nowhere and sat down beside him.

"Captain, I feel the need to point out that you should not have left the Medical Bay until the Doctor had dismissed you." These were the opening words to this particular conversation.

"Yeah, well I fancied some fresh air and a good seat." The blond responded coolly.

"The seats are allocated specifically, no one was likely to take it from you," the Vulcan pointed out, "And I find it difficult to believe you wanted 'fresh air' on a space station which uses artificial oxygen in its life support systems."

"For God's sake Spock... Just leave it!" he hissed abruptly, shooting a glare at his friend before he rolled his eyes and sighed heavily, "Sorry... Sorry I'm just a bit stressed out. Just... Just give me a break yeah?"

Spock stared at him for a long moment, inwardly debating whether or not he should question the Captain's ability to function properly while 'stressed', before he decided it would quite possibly earn him a broken nose and missing teeth, "Very well, I shall give you 'a break'." He responded curtly before he straightened in his seat and looked ahead.

Jim blinked but decided that he would take what he could get and relaxed in his seat again, or he tried to, but it just so happened that McCoy had gotten on the shuttle at that exact moment and time and decided to subject the Captain to several pre-flight checks before finally passing the dismissal order that the man was clear for air travel.

"Now, Jim," the man then began as he settled himself into the seat on Kirk's left hand side, "You are my patient until we find out what is happening to you and are able to do something about it. Is that clear?"

"Yes, Bones." The blond replied in a forced platonic tone.

"Let me explain that this means, if I say no physical exertion you stay in bed or you stay sitting down or you don't move around too much. Got it?"

"Got it." He nodded slowly.

"So, no running; no jogging; no walking over long distances; no raising your heart beat; no raising your pulse rate; no sports; no going clubbing and above all... No sex."

The Captain yawned, "Got it, fine, whatever, I don't care... Wait... Did you say no running?"

"What a wonderful time to develop a sense of humour, Jim, I'm serious." The Doctor said dangerously, "Don't forget I have the power to section you if you decide to back out of this agreement."

Kirk scoffed and rolled his head to the side so he was looking at the man, "Bones? I said I got it. I'm not backing out; I'm not even that bothered. I just want to get this over with."

"Yeah well... I'm a Doctor not a mind reader."

"Thank goodness for that." He muttered and looked away.

Once their shuttle had all thirty-six passenger seats filled they, among the other eight shuttles, departed from the space station on a premeditated flight path to San Francisco's Star Fleet Head Quarters.

For the life of him, Jim couldn't understand why this had been deemed so important that they had to go all the way to the HQ to have him seen by a couple of specialists, the board of Admirals and finally on to meet with Khan if it was regarded utterly necessary. It was that final bit he was both anxious and excited about. He had told the truth in his personal Captain's Log, and he did feel some strange connection between them. The whole thing gave him the creeps; he wasn't one to normally believe in paranormal stuff like 'connections' and 'links' between people. It just didn't make sense and it didn't seem... Logical.

Mentally shaking himself, Kirk decided to simply stop thinking about it, whatever was going to happen would properly happen whether he liked it or not. And if there really was a problem with this... Dormant strand of Khan's DNA then he would soon find out and it would be rectified. It was as simple as that. And after all, he didn't even know if he was going to have to see Khan face to face... Or even talk to him. It would be fine.

They landed fifty minutes later, instantly beginning to unload the passengers; Kirk, Spock, and Bones were some of the last to get off and although he desperately wanted to return to his Federation supplied room in the Federation controlled apartment block just across the road from the Federation run Academy, he found himself being escorted by his two body guards instead. It was like they didn't trust him.

It was only a quick walk, maybe ten minutes long in total, to reach the Head Quarters of Star Fleet, and once there Kirk felt himself becoming immersed in officials, scientists, doctors, students, Admirals, Captains... It was a network of people. Like a beehive, everyone had their little roles and each role worked towards the singularity; the singularity being that they were all working towards exploring the stars and finding out everything they could. Yes... It was like the Queen Bee was the Archives and every other bee was simply responsible for pouring more and more information into the Archive. What a wonderful life.

The three of them made their way to the fifth floor, the medical floor to be precise; where their Captain was immediately admitted into a side room and forced to remove his clothing and get changed into an awful itchy gown.

He was then left, laid on the bed in complete silence while the 'professionals' went to get everything ready. He had briefly overheard something about blood tests, urine tests, faecal tests, brain scans, CT scans, MRI scans, and a prostate examination. Needless to say none of them sounded overly pleasant to him at that exact moment. Despite that, he would keep his word to Bones; the best he could hope for was that he had a nice pretty nurse taking his bloods... And he would hope that they were kidding about the prostate examination.


They hadn't been joking, Kirk recalled miserably as he curled up under the covers of his hospital bed. It took hours for them to do all their bloody exams and by the end of it James Kirk was exhausted like he had never before been in his life, all the prodding; the pocking; the jabbing with needles, the probing of the prostate examination... It was too much for any man to bear. Admittedly he was used to having a lot of demand for his body, but this was just ridiculous!

He looked around as he heard the door open and all but pouted as he saw McCoy; Spock and strangely Carol Marcus entered his room. Their expressions weren't telling him anything, but then he knew all three of them had amazingly convincing poker faces. He sat up and reclined against his bed as he raised the back up slightly, interlocking his fingers and waiting for someone to speak as they all pulled up chairs beside his bedside.

When it appeared no one was going to speak, he decided to break the ice, "So, that was the first and last rectal exam anyone is ever giving me Bones. Seriously, if someone tries it again I'll be breaking their fingers. Got it?"

"Understood," the Doctor chuckled slightly before he cleared his throat, "So, we've been running a lot of tests-"

"I am well aware of that fact." He muttered

Bones glared as he was interrupted and continued, "Now, we don't have any conclusive results from any of the tests, but in your blood we were able to isolate the anonymous strand of Khan's blood which was affected by the radiation at Nagota, and I was correct to suggest that the dormant strand had been awoken."

"So you know what you already knew. So what?" Kirk asked as he folded his arms and raised an eyebrow expectantly.

"To figure out what the DNA does we definitely need Khan, awake and out of cryogenic sleep," the Doctor sighed in defeat, "We will need to take the same tests out on Khan and compare results to figure this out, but for now... You need to sit tight okay? I will be releasing you from the hospital but you have to stay at your apartment."

"You know you could just ask Khan about the DNA." Jim commented as he inspected his nails, "I think he would help."

"Why would he help you, willingly, Captain?" Spock asked suddenly, breaking his long silence.

He shrugged, "It is just a feeling I have. And what harm could it do? You can talk to him, ask him about it and then scientifically prove or disprove his thesis."

Spock and Bones shared a look for a long moment before Carol made a small coughing noise and spoke, "It's just a theory but... perhaps the questioning would be best coming from the Captain? I mean, Khan has only ever offered his assistance to the Captain in the past, despite it being for his own gain it was always in his presence that he told us anything."

The three men stared at her for a moment before Spock nodded, "That is logical."

"What? Spock, you can't agree that this is a good idea! Last time they saw each other Khan tried to kill him!" Bones exclaimed.

"But he did not. He instead decided to transport him back to the Enterprise and..."

"Blow us all up. Yes, that is so much better." McCoy growled, "Bloody green-blooded hobgoblin."

"I'll do it." Kirk said simply, "I will talk to him. It will be a secure environment anyway so it is not like anything bad is going to happen is it?"

"But Jim-"

He held up a hand, "Bones... I know what you are getting at. Really I do and if it wasn't necessary I wouldn't do it but I agree with Miss Marcus, Khan has always been happier to talk to me directly. I think if there is a chance that he will talk, then he will want to talk to me."

The Doctor hesitated for a moment before he sighed heavily, "Fine. Fine... Khan will be woken up as soon as we get permission from the Admirals and then... Then you can go and visit him."

Kirk paused for a moment, "Is he already here? They've brought him to San Francisco?"

"Yes." He said a little bitterly, "He's in a room down the hall. He's still in his cryotube at the moment."

"Oh... I didn't realise." He shrugged it off and smiled, "So, all steam ahead my good Bones, off you pop and talk to people."

McCoy rolled his eyes and threw his hand in the air in disbelief at his friend's attitude to everything, it was like nothing penetrated his bloody armour; nothing got skin deep. He retreated from the room before he was overwhelmed by the desire to kill the man himself.

He paused by the door to Khan's room, the one right next to Jim's and looked through the glass door and the black haired man who was sitting silently in the bed, his eyes were closed; concealing those piercing ice blue eyes that seemed to penetrate into your head and make it seem like he knew what you were thinking. But he could tell that the man was tense, ready for action, ready to fight if he had to. Yet he hadn't. He hadn't fought a single man, woman or alien species since he had been woken up.

Bones didn't like lying to Kirk, but there were some things the guy was better off not knowing. Like the fact that Star Fleet had woken Khan the moment they had received the report on Kirk's condition, or like the fact that they had it on record that the first word out of Khan's lips was "James", or like that fact that Khan had been quiet and contented and very unlike the man they had previously encountered. Unless they were counting the man's time in the brig, because he had been very calm then... Too calm. Just like now.

It made him very uncomfortable. So uncomfortable, that he could throw up.