Coming Home
By Xanthe
Part One: Trouble with a Capital 'T'

Colonel John Sheppard knew, from the moment he first met Dr Rodney McKay, that the man would be trouble. He wasn't sure how, or why, or even what form that trouble might take, but after nearly twenty years in the military, John had an instinct for trouble, and Rodney McKay was it - with a capital 'T'.

John was standing in Lady Elizabeth's office, going through the personnel files of the people they were taking with them on the expedition to Atlantis, when someone knocked on the door and then barged in without waiting for a reply. John stiffened; Lady Elizabeth was their leader, and, although he'd only known her for a few days, John had a lot of respect for her, so he didn't appreciate someone so rudely interrupting their private meeting - especially not the dishevelled man who brushed past him, shoving him to one side in his eagerness to get Elizabeth's attention.

"Is this the guy?" the newcomer demanded, glancing at John as if he was something he'd stepped in. "Isn't he a bit young to be in charge of the entire military side of this expedition? And what's with the hair? Oh never mind. You said he has the ATA gene? Because if so, you have to lend him to me. Carson is driving me insane and besides he nearly destroyed General O' Neill's transport with one of those drones, and you know if anything had happened to the General then Daniel O'Neill would have blamed *me* and then there's no chance I'd get anywhere near Atlantis - I'd be strung up in little pieces somewhere while he carved into me with a blunt knife. That man is the most possessive sub I've ever met."

John blinked, and glanced at Elizabeth, overwhelmed by the whirlwind of chatter.

"Ah, Colonel Sheppard - I should introduce you to our Head of Science - Dr Rodney McKay," Elizabeth said, with a wry grin. Sheppard took a second to process that *this* man, standing here, fingers clicking together impatiently, was the very eminent Rodney McKay, a scientist of outstanding brilliance - according to his personnel file at least. The man in front of him had long, unkempt, wavy hair, most of which was standing on end, as if he'd just spent several days running his hands through it - maybe he had. He had three days worth of stubble on his chin, and was wearing a faded blue expedition sweater and a pair of black pants with a coffee stain on the thigh. He looked sort of unkempt, as if he had long since stopped caring about his appearance and didn't expect anyone else to, either, and yet… John noticed a pair of bright, intelligent, if guarded, blue eyes, and a crooked mouth that looked as if it could spit out insults as soon as give you the time of day. Yes, the man was definitely Trouble.

"Dr McKay." John nodded, and held out his hand in greeting. McKay gave him a withering look.

"Yes, yes, time for that later - at the moment I need you - or rather I need that gene of yours. Come with me."

It was an order, and so peremptory that John found himself glancing at Elizabeth in shock, seeking her approval to end the meeting. She just gave a little grin and nodded her head in the direction of the door.

"I think Rodney's need of you is more pressing than mine," she murmured. "We can catch up on this later."

John gave her a polite nod, and then followed on after the scientist. It wasn't his usual style to notice such things, but he couldn't help but think, as he walked down the hallway after the other man, that Rodney McKay had a very nice ass.

"So you, apparently, have the ATA gene. It doesn't seem very helpful that one of the military boys should have such a strong manifestation of the gene when I'm the one who has to get this stuff working but I suppose we have to live with that. Carson is working on some new treatment that should resolve that issue for us but he's going at a maddeningly slow pace at the moment. I don't see what's so hard about it - it's not as if what he's doing is *real* science - but I suppose we have to accept that he knows what he's doing. By the way, do they *allow* hair cuts like that in the military? I thought you all had to have buzz cuts which is rarely a good look for anyone but I assumed it was some kind of weird bonding ritual you went through, and here's the chair so if you'd like to sit down please?"

"What?" They had come to a halt beside a large, ornate chair, situated in the centre of a little chamber, and Rodney's request had been so jumbled up in the rest of his stream of consciousness speech that John had to take a moment to process it.

"Chair. Sit," Rodney said slowly, as if talking to an imbecile, or a dog. John gazed at him steadily for a moment. He had been in the military for most of his adult life and he was more than used to taking orders, but not from scruffy scientists who seemed to be lacking a social skills gene. Rodney blinked, then looked at John as if seeing him for the first time. "If you wouldn't mind," he added, in a more polite tone of voice. John gave him a smile.

"Not yet," he said. "Firstly, I want you to tell me why you need me for this - and what's supposed to happen when I sit in that chair? I know I've got some kind of a genetic thing going on which means that I can activate Ancient technology but I don't want to make any mistakes, or do the wrong thing."

"Oh god. You're not afraid of it are you?" Rodney rolled his eyes. "It's bad enough dealing with Carson but at least he's a doctor and has an excuse for being uncomfortable around weaponry. I'd have thought you would be delighted to get the chance to be in control of this kind of destructive power."

"Really?" John raised an eyebrow. "I don't know what you know about the military, Dr McKay, but personally I prefer to have a thorough understanding of my weaponry *before* I use it."

"Really?" Rodney raised an eyebrow back at him. "As a matter of fact I know quite a bit about the military and I have to say that's not my experience of you military boys," and there was something about the way he said it, and the sour little bark of laughter that accompanied that comment, that made John frown. He wondered just what experiences the scientist was talking about.

"Explain it to me," John told him, softly but firmly, "and then I'll decide if I want to sit in it."

Rodney rocked back on his heels and gave John an assessing look, clearly realising that this wasn't someone he was going to be able to push around, and that he'd have to at least give some kind of explanation.

"You won't understand," he warned.

"Try me," John grinned. Rodney's eyes narrowed, and then, obviously deciding this was a challenge and he was happy to seize the gauntlet, he opened his mouth and launched into a detailed explanation of how the chair worked that was so technical John had to concentrate extremely hard to follow it. However, despite all his bluster, the scientist actually had a very good way of explaining things, and there was something rather amusing about his style of speech and his frequent snarky asides that made John smile. He came to an end of his explanation and then stood there, looking at John with an expectant smirk on his face, clearly expecting him to have been completely lost in all the technobabble.

"Thank you." John inclined his head towards the scientist. "So basically you're saying that these drones are telepathically controlled and when I sit down I have to be careful not to unleash another one?"

"Something like that," Rodney grunted sourly, obviously annoyed that John had grasped the central concepts so easily. "Especially if General O' Neill's helicopter is anywhere nearby. We really don't want any harm to come to him or…"

"Or his husband will come after you with a blunt knife. I remember," John grinned. "Sounds like the general has his hands full with that one."

"Yes, well, I really don't have the least interest in their particular dynamic," Rodney snapped, but John caught a flash of something in the scientist's blue eyes - something naked, something hurting, and that surprised him because this man was so outrageously rude and brusque that John would never have suspected him to have a sensitive side. There was clearly a whole lot more to him than met the eye. John put him on his mental list of people to watch on this expedition.

As it turned out, John didn't get a chance to watch anyone for the next few weeks as they were beset by a series of crises from the minute they walked through the gate into the Pegasus galaxy. The city welcomed him like a returning son, lighting up at his every step, only to start crashing all around them as the power ran out. John led an expedition offworld to find refuge and instead encountered a hostile alien species that captured half his team, forcing him to lead a rescue mission, and when they returned to Atlantis, the city activated her own failsafe device by rising from the depths of the ocean into the clean, clear air. So much happened in such a short space of time that John almost forgot about Dr Rodney McKay - until the incident with the jello.

"Colonel Sheppard - take a seat." Elizabeth gestured with her hand at one of the spare chairs in her office. She looked tired, and John wasn't surprised. They'd all been running on empty for the past few days. She was dressed, as usual, in the tight, dark red, leather uniform suit that showed off her slender frame to perfection. John had worried initially about how he'd get along with her. They were both tops, which wasn't a problem - although John doubted he'd have had a problem if the leader of the expedition had been a sub, either. He'd known some tops with terrible leadership qualities and some subs who truly excelled in that area and he knew sexual inclination wasn't any guide as to how well someone performed in their job. Luckily, Lady Elizabeth Weir had proved herself to be a thoughtful kind of leader, and although he didn't always agree with her more cautious decisions, he was glad that she was someone he could work with, and respect. John wondered for a moment whether she had taken a sub - he was sure that half the available subs in the city would jump at the chance because she exuded an air of capability and control, but he also knew that it wasn't always easy taking a sub from among people you worked with. Still, he didn't like the idea of her being lonely - a good leader needed an attentive partner, whether sub or top. John was feeling that lack in his own life right now, but he had nobody but himself to blame for that. He'd had some great relationships with a variety of willing and compliant submissives, but the truth was that he'd never been in love and he was beginning to despair of ever finding someone he connected with on anything other than a sexual level. He longed for the soul-deep connection he'd seen other couples enjoy - including his own parents - but somehow it had just never happened for him and he was beginning to wonder whether it ever would. Maybe he was asking for too much but he knew that he couldn't fake it. He'd bent many beautiful bodies, both male and female, to his will, enjoyed them for the taking, and loved doing it too, but he had reached an age where he wanted more than that, and as a result he'd been celibate for over a year now.

"What's going on?" John asked, seeing Elizabeth sigh heavily as she flicked through a file, before handing it to him.

"There was some kind of fracas in the mess hall yesterday," she told him. "One of your men - a Sergeant Bates? - sustained a cut to his forehead requiring four stitches."

"I heard about that. I assumed it was just some horsing around," John commented, surprised that this minor issue had made it to her desk. "I'll deal with it, my Lady," he said in a grim tone, getting to his feet. He'd been so busy dealing with one crisis after another since they arrived that he hadn't had a chance to establish a clear sense of discipline - and the men under his command were all new to him. This was his first major command, and he was aware that he'd landed it partly because of the ATA gene. Not that he hadn't proved himself in the field of combat, over and over again, and the military had commended him for his leadership abilities on several occasions, but this - out here, in another galaxy - this was a whole new ball game.

"It's not that simple," Elizabeth told him, with a strained smile. "I asked you here because Sergeant Bates has made a formal complaint against one of the civilian members of the expedition - and now I have to decide what to do about it."

"Oh." John sat back down again. Setting up a judiciary system and formal punishment room hadn't exactly been top of their list of priorities when arriving here, but it was clear that it had just been shunted up the list. "So what happened?" he asked, flicking through the complaint that was in the file that Elizabeth had given him.

"It's not easy to tell - I've only got Sergeant Bates's version of events and there were no witnesses save for a group of military personnel and…" Elizabeth gave another sigh, "Dr McKay."

"McKay?" John looked up in surprise.

"Yes. Bates alleges that McKay launched an unprovoked attack on him, and, uh…threw a plate of jello at him. The rim of the plate cut Bates's forehead - hence the need for stitches."

"My god - if I'd been wounded by a flying plate of jello I'd keep quiet about it, not launch a formal complaint!" John laughed. Elizabeth gave him a wry smile.

"Unfortunately, Sergeant Bates seems to be taking this very seriously. He's pressing for punitive charges against Dr McKay," she told him.

"What?" John shook his head. "Oh god. We could do without this after all we've been through these past few weeks," he muttered. "So what does McKay say about all this?"

"I don't know. I thought I'd speak to you first - find out a bit more about Sergeant Bates. The facts seem incontrovertible though," she said, her hazel eyes weary. "The other marines in the mess hall at the time all say that McKay threw the plate at Bates."

"So, what are you thinking of doing?" John asked her slowly, not liking where this was going but this wasn't his decision - it involved a civilian so it was hers.

"I'm not sure I have a choice," she replied. "I don't like it, but…we're out here all alone, John. We have to make it clear to people that the rules are the same here as they were on Earth. I can't go bending them for anyone - particularly for a member of my team. It'll look like favouritism. If we let this slide, then I'm worried that things will fall apart and anarchy will set in. I don't want anyone thinking I'm a weak leader - we both know that's fatal for morale and for discipline generally."

She sat back down at her desk and looked at him, her arms spread in a gesture of defeat.

"I'm unhappy about the idea of a senior member of the civilian team being publicly disciplined," John told her, shaking his head. "Dr McKay is a man who should command respect, and that'll be hard for him after something like this."

"I know, but what can I do?" Elizabeth gazed at him helplessly.

"Well, talk to McKay for a start - find out his version of events," John told her. "As for Bates - I can't give you much help there. I barely know him. I've read his file though, and he's a by the book kind of guy. Not very imaginative, but does his job to the letter - perhaps he takes that a bit too far at times, but he's solid."

"That's what I'd heard too," Elizabeth nodded. "All right - let's get Rodney in here and see what he has to say about this."

Rodney McKay burst into the room a few minutes later, looking as dishevelled as ever. John wondered whether the man ever shaved - or changed for that matter. He was wearing a coffee-stained blue tee shirt, and his eyes were red-rimmed, as if he'd been up all night working on something. His hair was as startling as ever - standing up in manic tufts all over his head.

"Well - what is it?" he demanded of Elizabeth. "I've just spent the past seventeen hours working on hooking up the damn naquada generators to take over the massive job of heating and lighting this city now that the ZPMs are all defunct, and could do without the interruption thank you very much."

John winced. He longed to get hold of Rodney McKay and shake some politeness into him, but Elizabeth seemed used to his manner and she just smiled at him, that strained smile of a leader under pressure.

"Rodney, sit down. We need to talk," she told him.

"Oh god. That's never a good phrase," Rodney sighed, sitting down in the seat beside John. "This isn't about that stupid incident in the mess hall yesterday, is it?"

"I'm afraid it is," Elizabeth told him. "Sergeant Bates has pressed charges against you."

"Oh WHAT?" Rodney looked outraged.

"He did need four stitches in his head, Dr McKay," John said. "So I think he has a right to press charges, don't you? Unless you're saying it was an accident?"

Rodney turned to look at him, those blue eyes of his flashing. "Well, you're military, so of course you'd take his side, Colonel," he snapped. "What's Bates saying, Elizabeth?"

"That you threw a plate at him."

Rodney stared at her for a moment.

"Is that true?" Elizabeth prompted.

A defeated look crept into Rodney's blue eyes and he shrugged. "Yes. I suppose it's true," he said softly.

"And?" Elizabeth waited but Rodney just shrugged again. "Come on, Rodney, work with me here. Were there any extenuating circumstances? Anything that makes this look less bad than it is?"

Rodney thought about it for a moment. "Things were said. It was heated. I didn't honestly intend to hit him with the plate but I admit I lost my temper and threw it in his general direction. Of course if I'd actually been *aiming* for his head it would undoubtedly have sailed over it by several inches because although I'm a genius my aim is crap - as is my ability at competitive sports. It was a freak accident - nine times out of ten I doubt the plate would have broken any skin but it sort of ricocheted off the wall and broke and the ragged edge caught him on the forehead. You're right though - he did need stitches and I accept full responsibility for that," he said quietly. Elizabeth sighed and sat back in her chair.

"What kinds of things were said, Dr McKay?" John asked, picking up on something the scientist had said. Rodney turned to look at him again, and this time those blue eyes of his were guarded, and he gazed at John with a distrustful expression.

"It doesn't matter. I clearly behaved…inappropriately. I'll apologise to the sergeant."

"It's gone beyond that, Rodney," Elizabeth told him. "He's asked me to take punitive action."

Rodney thought about that for a moment and John gazed at him, fascinated by the play of emotions that flitted across the other man's expressive face, from dismay to humiliation to, finally, resignation. His jaw tightened into a jutting display of tense bravado and he got up. "Well, that's your decision, Elizabeth," he said softly. "Now, if that's all I have work to do. Whether the military boys like it or not, I'm the one who keeps the lights and heat on around here."

"Rodney!" Elizabeth called, and he paused by the door, his back stiff. "You do know what I'm talking about here, don't you?" she said. "This will be a public disciplinary. I don't want that any more than you do and I don't think it sets a good example if a senior member of the expedition is in this situation - do you?"

John watched the tense play of muscles in the other man's shoulders as he stood, his hand on the door. Finally, Rodney turned.

"No," he said. "I don't think it's a good idea for any number of reasons, not least of them being my concern about my own ass, but I also know that if you have to throw me to the wolves to keep this base running efficiently then you will, and I do understand that. I do!" he repeated fiercely, as she opened her mouth to protest. "I'm not going to put you in an awkward position, Elizabeth. Do what the hell you want. You will anyway." And with that, he left the room, slamming the door shut behind him.

Elizabeth turned to John, her arms open in a gesture of despair again.

"There's no helping some people," John told her, with a shrug. "Especially if they won't help themselves."

"You think I should authorise the punishment?" she said, stroking her neck anxiously, as she always did when she was uncertain.

"I don't think you have much choice. The guy admitted he threw the plate and he wouldn't give us any extenuating circumstances - there's not much else to be done, is there?" John said, giving her a sympathetic smile. Privately, he couldn't help thinking that Rodney McKay was such an obnoxious piece of work that it would do the man good to have some humility drummed into him.

"All right. You'd better get a punishment room set up. I'm keeping this light though - enough to satisfy Bates, but no more," Elizabeth said grimly.

"Agreed." John nodded. He walked out of the meeting with a heavy heart; this was not a good beginning to their time on Atlantis.

John went back to his office and studied his personnel files, while deciding what to do next. Bates was part of a close knit group of marines who had been working with the expedition team for months before John had even come onboard. He was deputy head of security on Atlantis, reporting in to John's second in command, Major Lorne, and he took his job very seriously, but there had never had any complaints about the man.

John decided to speak to Major Lorne first. He didn't know the major very well, but he liked and respected what he'd seen of him thus far - and, more importantly, Lorne knew these men, having worked with them for the past year or so. Lorne didn't tell him any more than John knew already though - that Bates was solid, and, although the sergeant was a fairly humourless individual, with a vindictive streak, Lorne couldn't imagine him making this whole thing up.

With a sigh, John dismissed Lorne and made a call on his radio asking Sergeant Bates to come and see him.

"You've made a complaint about Dr McKay," John told him, gazing at the man's head - he had a dressing over his left eye, and a slight bruise was visible around the edges.

"Yes, sir." Bates nodded.

"Care to tell me what happened?"

"He came into the mess hall, sir, and he was angry because we'd eaten all the blue jello," Bates told him. John tried not to laugh out loud - that sounded very like Rodney McKay. "I pointed out to him that if he wanted the good stuff he should have got there earlier so he'd just have to settle for the green. He said he'd been working all night just to keep the place running and he expected a little gratitude. I told him we were all doing our jobs…and that was when he threw the jello at me, sir," Bates told him.

John sighed. This all sounded entirely plausible. "Was it necessary to make a formal complaint though, Sergeant?" he asked. "We all have to live together after all."

"I'm going to be permanently scarred because of one man's petulance, so yes, sir!" Bates growled. "I think it was necessary."

"Could I talk you out of it?" John asked, leaning back in his chair, feeling tense about even suggesting it because this was Bates's prerogative, and he didn't want the other man to think he was trying to pull rank on him over this.

"No, sir! I don't think you can," Bates told him firmly.

John sighed. "Very well. You can go," he said. He called in a couple of the other men who'd been witnesses, but they all said the exact same thing, so John had to conclude, reluctantly, that there was nothing further to be done and that Dr McKay would just have to take his licks.

The disciplinary was scheduled to take place the following day at ten a.m. John didn't usually attend public disciplinaries - these things were best dealt with privately, in his view - but Rodney didn't have a top to speak for him and refused to speak for himself. John didn't even know if the man was a sub or a top – but his top radar picked up on something about the scientist which made him suspect that McKay was more likely sub than top. Apart from anything else, the incident with the jello had taken place in public, and by law Bates was therefore entitled to request public redress. John attended the disciplinary purely out of duty; this had taken place on his watch and some of his men had been involved. He also wanted to get a feel for the atmosphere on the base - to see if people would feel justice had been done, or whether a more ugly mood was brewing.

John entered the punishment room and then paused in surprise - the place was packed to the rafters so he guessed that he wasn't the only one Rodney had irritated with his brusque manner and snappy comments. As he took his seat and glanced around, he realised the majority of the people present were his own men - there were a few people from the civilian side of the expedition, but, he noted thoughtfully, none of Rodney's own team was present. He was glad about that - it wouldn't be easy for the man to maintain his authority after this, and he was still their Head of Science after all.

Elizabeth was there, sitting at the back, her expression subdued. John gave her a half salute as he went in, and she acknowledged him with a little nod. He wasn't surprised that she wasn't handing out the punishment herself. As their leader it was her prerogative but it was more usual to delegate that kind of task to a trusted member of staff. He *was* surprised to see that she'd chosen Peter Grodin for that job though - Grodin was on Rodney's staff, under the Head of Science's direct command, and John wasn't sure it was a good idea for him to be the one doing this, but he guessed that Elizabeth had a pretty small pool of people to choose from on a base this size. Grodin stood in the centre of the room, examining the equipment they'd brought with them, which they hadn't had to use to date. It was standard judicial stuff - a sturdy frame, and a case of implements. Grodin took out a light paddle and swung it through the air a couple of times, to the obvious delight of some of the military personnel in the front couple of rows.

On the dot of ten a.m. Rodney McKay appeared in the doorway. He looked as tired as he had done the previous day - although John suspected this was more because he'd spent another night working on the naquada generators than because he'd been up all night worrying about the disciplinary. The scientist paused in the doorway, and then blinked, several times, as he took in the crowd in the room. John felt a pang of sympathy for the man, despite himself. It couldn't be easy to realise that all these people had come here to witness him being punished - or that they would take pleasure in it. Rodney's eyes were glinting, and he gave them all a dangerous, baleful glare as he stepped into the room, daring anybody to say anything, his jaw pushed out to the maximum, in a full tilt of defence. None of this had much effect on the marines in the front couple of rows though - they laughed out loud and gave some ribald catcalls. John cleared his throat - loudly - and the jeering subsided.

Rodney stepped over to Peter Grodin and stopped for a moment to say a few words to him. John couldn't hear what was said but Peter managed a forced smile and he nodded at whatever it was Rodney was saying to him. Then Grodin said something in return, and John guessed he was reading Rodney his rights, going through the usual disciplinary preamble. John wondered if the scientist had ever been publicly punished before. Plenty of people managed to go a lifetime without getting into any kind of judicial trouble, although somehow John doubted that Rodney was one of them. During his teenage years, John had earned himself a couple of public disciplinaries. They had been carried out by a bored cop in the small public punishment arena back in his hometown in front of a couple of equally bored witnesses and his own disappointed and disapproving parents. That had been bad enough, so he couldn't imagine how unpleasant it must be to be in Rodney McKay's shoes right now.

Grodin finished whatever it was he was saying to Rodney and then he gestured to the punishment frame. Rodney gazed at it with distaste, and then, with a mulish look on his face, he went over to it and loosened his belt and fly, before sliding his pants and boxers down his thighs until they were resting just beneath his buttocks. Then he leaned forward and took hold of the handles on either side of the frame, so that he was bent over, his ass jutting out.

The punishment frame was deliberately designed for this purpose. It was a large, curved piece of equipment with a padded bench. The only part of the miscreant's body visible from the front was his face and shoulders - it didn't form part of the punishment that any more flesh than that was on public display, although from some angles a little bit more was certainly visible. The only one who got to see any naked flesh full on was the person performing the punishment, and Grodin stepped up, slapping the paddle lightly against his own hand. John glanced at his men, who were watching with rather more rapt attention than he liked. He caught sight of Bates, and noticed the smugly satisfied expression on the sergeant's face. John didn't like the look Bates was giving Rodney, and he glanced back at the scientist. Rodney gazed out at the audience, those blue eyes of his hiding absolutely nothing of the sheer humiliation he was feeling right now, and then he did something that John would never be able to get out of his head, for as long as he lived. It wasn't much - but there was something about it that made John sit up and really notice this man for the first time. Rodney turned his head, and his eyes made the briefest of contact with John's before he rested his face sideways on the punishment frame. His face was now angled, unintentionally, in John's direction and John watched as Rodney slowly closed his eyes and then opened them again, and then he lay there, and there was an expression in his eyes of such sad acceptance that John's breath caught in his throat. Suddenly this had gone beyond duty for John, beyond his faintly bored witnessing of an unpleasant man getting his due. The expression in Rodney's eyes seemed to say, "Right. Yes. Of course. Here we go again." And rather than looking like the brusque, sarcastic scientist John thought he knew, now he resembled nothing so much as a lost, forlorn puppy, friendless and without a home. That realisation took John totally by surprise and now his interest in the proceedings was no longer dispassionate. Now it felt personal.

The moment passed and Grodin raised the paddle and brought it down firmly on McKay's ass. John's gaze never left the scientist's face, and Rodney didn't so much as make a sound. His expression never faltered, either - there was no acknowledgement of the swat at all, except in those sad blue eyes. John felt his hands clenching into fists. This was wrong. He wasn't sure why, or how, just that it was. This shouldn't be happening like this - he didn't want to witness this event. He had seen plenty of people punished before - hell, in his job he'd had to discipline countless unruly men himself over the years, and he'd never had a problem with it, but this…THIS…this was wrong. Not because Rodney didn't deserve it, because John was by no means convinced on that score, but because John felt so profoundly uncomfortable that so many other people were witnessing it. To be honest, he couldn't have articulated what his emotions were, just that it angered him, and he felt a primal instinct rising inside him, wild and furious. That instinct warred with something else, something infinitely more tender and protective, and the two of them combined to make his fists clench and unclench convulsively, and his breath hitch in his throat. Nobody should be touching Rodney like this, damnit, because…. He had no end to that sentence - he just knew that the scene in front of him outraged him beyond belief.

Grodin raised the paddle again and delivered another swat, and again there was no reaction from Rodney, save for a little spark of distress in those blue eyes. John couldn't take his eyes off the other man's face. His attention was totally rapt, and he felt as if he was hardly breathing. Rodney's expression was dead, and his body was loose and unresisting, as he took the eight licks Elizabeth had ordered. He didn't once cry out, or say anything. He barely took any notice of the crowd, as if they weren't there, and John sensed their mood change. In the beginning they'd come here looking to enjoy the arrogant scientist get his comeuppance, but, in the face of Rodney's innate dignity and sad sense of calm, there was nothing to enjoy. It became just another punishment session, and they'd all seen or endured enough of them to know how it went. The punishment came to an end, and Grodin went over to Rodney and murmured something into his ear. He didn't touch Rodney - it wasn't protocol - even though John knew, as a top, how hard it must be not to give some kind of reassuring comfort after this kind of event. But Grodin wasn't Rodney's top and didn't have the right to touch him - John doubted that Rodney would have welcomed any such patronising displays of concern in any case. The scientist pushed himself away from the frame, pulled up his pants, fastened his belt, said a couple of words to Grodin, and then left the room, without once looking at the assembled crowd.

John wasn't sure what he was doing but somehow he found himself getting to his feet and running out of the room after the scientist. He was vaguely aware of the marines getting up and starting to talk and laugh amongst themselves behind him, but he ignored them. He chased up the hallway and found Rodney waiting by the transport at the far end. Having run after him, John suddenly found that he had nothing to say, and he hesitated by the transport, gazing at Rodney's flushed face.

"Come to gloat, Colonel?" Rodney asked, in a tight little voice. "Your men must be pleased - they always enjoy it when I'm the floorshow."

John stared at him, shocked by the bitterness in Rodney's voice, and by his misunderstanding of John's intentions. "Not here to gloat, no," John told him, in a quiet voice. "I thought you took that with amazing dignity actually."

A look of confusion flooded into Rodney's eyes and he rocked back on his heels, still glaring at the colonel.

"Dignity. Right. Okay." He shook his head, as if amused by some private joke.

The door to the transport opened and Rodney stepped inside.

"Wait!" John said, grabbing hold of Rodney's arm. "You should go and see Dr Beckett," John told him. Rodney stared coolly at the hand John had on his arm.

"Take your hand off me, Colonel, or I'll bring charges of my own," he hissed. John let him go, as if stung.

"I didn't mean…" he began. "I'm just saying - those swats were hard - you should see Beckett."

"It was only eight swats. I'm sure I'll live. Besides, I have work to do," Rodney growled at him and then he thumped his hand on the door panel and it closed, shutting John out.

John stood there for a moment. Something about this had been wrong, very wrong, and he realised, with a start, what it was. It was him. He hadn't done enough to investigate this situation. Oh, sure, he'd had a word with Bates, and some of the other marines, but he hadn't done any further digging - he'd just taken the sergeant's words at face value. There was something else going on here, something that had to explain the ugly jeering he'd witnessed in the punishment room when Rodney had made his entrance.

John wasn't sure where to start digging, but he found himself going down to the infirmary. Rodney wasn't there, although John hadn't expected him to be - the scientist had been very clear on that topic. Dr Beckett was alone down there, gazing at something under a microscope. John paused, and then went over to him. He'd met the doctor a few times and he liked the jovial Scotsman with the clear blue eyes and sympathetic bedside manner. Carson was a no-nonsense kind of man, and John was fairly sure he topped, judging by how well he managed to deal with some of the more difficult patients in his infirmary, but he was also essentially kind-hearted and John liked that about him.

"Hey, Doc. What's going on?" John asked, perching on the side of Carson's desk. The doctor looked up, and gave him a brief, tight smile.

"You tell me," he said. "I heard there was some action in the bear pit this morning. I suppose you've just come from there?"

John frowned. "You're not in favour of public disciplinaries I take it?" he asked.

Carson shrugged. "I accept that sometimes they're necessary," he said. "But sometimes they just seem like entertainment for the masses, and I for one don't get off on public humiliation."

"Well, I'm with you on that one," John told him, shaking his head. "That's why I'm here. You've known Rodney McKay for longer than anyone else. What's he like?"

"Brilliant, obnoxious, irascible, irritating, arrogant, condescending, stubborn and completely and utterly without guile. Why?" Carson asked.

"I'm not sure," John mused. "Do you think he threw that plate at Bates the other day?"

"Without question," Carson grinned. "He admitted it, didn't he?"

"Yes he did…but he didn't say why." John chewed on his lip thoughtfully. "Carson - what's Rodney's story? I gather he doesn't have a top's protection right now – I mean, I’m assuming he’s a sub? I get that vibe off him."

Carson sat back in his chair and gazed at John, those blue eyes of his piercing right through him.

"Are you asking because you think it'll throw some light on your investigation, or because you have a personal interest in him?" he asked cautiously.

"Does it matter?" John threw back.

"Aye, it matters," the doctor told him firmly. "I'll not have anyone screwing around with Rodney. He's been through enough. So if you were looking for a sub to play with, then I'd advise you to take it easy and go slow. He'll likely bite your hand off as soon as kiss it though, so he'd be a challenge if that's where your interest lies."

"He is a sub then?" John put his head on one side. Carson sighed.

"Aye, he is. I think he struggled to come to that conclusion, but he's comfortable enough with it now."

"What did you mean by him having gone through enough?" John asked carefully, unsure why he felt such a sense of relief at finding out for sure that Rodney was a sub. Carson sighed again.

"Colonel, I haven't known you very long but you strike me as a good man, so I'll tell you, but please keep this confidential," Carson requested. John nodded. "Okay then…Rodney is…well, you have to get to know him to understand him, but he's a good man. He's about the best friend I have out here, and he'd do anything for you - he just doesn't want you to know that. He hides behind all that bluster and sarcasm but he'd go to the wall for you if you let him. I meant what I said just now - he IS obnoxious and arrogant, and he says the most terrible things, but he's also kind, funny and…well, sort of lovable underneath it all, if he lets you get close enough to see it."

"Did you…did you ever play with him?" John asked, wondering why he felt a tight knot in the pit of his stomach as he asked that question. Carson shook his head.

"We got close to it one night when we were both drunk, but it wouldn't have been right. He's a handful and I like a quieter life. I'm not a heavy top, either - he's someone who needs taking down and I prefer my subs respectful and worshipful rather than mouthy and mixed up."

"And the bit about him having gone through something?" John wanted to know.

"His parents were a nightmare. They screwed him up good and proper and the poor lad never had much by way of affection there. They died in a car crash when he was just eighteen. He was a graduate student at MIT by then but he came home to look after his little sister and continued his studies at the University of Toronto. He fell out with his sister a few years back, and he hasn't spoken to her since then which cuts him up deep inside because he loves her to bits although he'd never tell you so. I used to tell him to write to her but he's a stubborn so and so and he wouldn't. His argument with Jeannie upset him more than he cares to admit and he was all at sea for awhile and fell into some bad relationships. I know there was a woman who was quite abusive towards him, and some chap he ran rings around until the poor bastard gave up and threw him out. Rodney took that quite hard, although I didn't blame the man - Rodney is a handful, as I said. Then there were a series of one night stands that went really badly. Rodney is a genius - and he doesn't always understand how other people think or feel. He's an odd mixture of superiority complex combined with a genuine lack of understanding as to why anyone would love him, and that makes it hard getting through to him sometimes. He's a good man, Colonel, but he's been given a hard time by some of the people on this base."

"Who - and why?" John leaned forward, sensing he was about to learn something here.

Carson sighed. "Rodney went out with one of the military lads for a couple of weeks a few months or so ago but it ended badly. The man in question wasn't the brightest button in the box and Rodney needs to be with someone smart. And you know Rodney - he doesn't mince his words so his lover was in no doubt at all about what Rodney thought of his intelligence. As a result, he spread some rumours about Rodney that I'm certain aren't true. He said that Rodney was a crap submissive, that he wasn't worth playing with, and that people shouldn't touch him with a bargepole. Rodney was genuinely bewildered by all this, I think. He might be a challenging sub but he does like to be the best at what he does so I'm sure he's eager to please and tries his hardest. A lot of people miss that about Rodney.” Carson sat back in his chair and gazed at John. “Are you sure you want to hear the rest of this?” he asked.

“Very sure,” John said firmly.

“It doesn’t reflect well on your men.”

“Then I’m even more sure,” John growled.

“Okay then.” Carson nodded, leaning forward as he continued. “The military lads had it in for him from then onwards - they never wasted an opportunity to taunt him about his lack of sexual prowess, or anything else that they thought would needle him. Sometimes it got really ugly - and that's just the stuff I overheard. I imagine it was much worse when there were no witnesses. Rodney took it all with rather more patience than I'd have expected. He had a tough time at school - he was too bright to fit in, and he got bullied quite a bit. He couldn't tell his parents about the bullying because they showed so little interest in him so I gather that he led a rather lonely existence. This thing with the military lads - I think it's almost what he's used to, like what happened to him back in high school, and that's why he put up with it. I wasn't surprised it finally spilled over though - Rodney's put up with a lot over the past year or so, and that particular plate of jello was a very long time in coming."

Carson sat back again and surveyed John intently. "So that's your story. Do with it what you will, but, if you're the kind of man I think you are, you'll do the right thing."

John gazed at him, feeling somewhat winded, and sickened to his stomach by what had happened that morning. That hadn't been justice - that had just been more bullying, and it had to stop. Nobody got away with behaving like that on his watch.

"Why didn't Rodney say anything about all this when Elizabeth called him in to defend himself?" he demanded.

"Well, I can't say for sure but I'm guessing it was because you were there," Carson pointed out. "You're military after all, and after what he's been through Rodney doesn't have a great deal of trust left in the military. I presume he just thought you'd take their side. Also - it's not exactly an easy thing to talk about, and the man has his pride. He'd find it hard to admit to the two highest ranking tops on this expedition that there are rumours circulating that he's a bad sub."

"Damnit!" John growled, leaning back and thumping his fist on Carson's desk, angry with himself for not knowing any of this and for unwittingly putting Rodney is such a difficult position. "This man Rodney was seeing - is he on the base?" he asked, wondering why that spark of jealousy was flaring in his belly again, white hot.

"No. He didn't make the grade and was reassigned before we left - but Bates was his best friend," Carson told him pointedly. "I suspect Bates also thinks Rodney is the reason why his friend wasn't part of this expedition but that's all bollocks, if you'll excuse my Scottish, because Rodney didn't have any say in the selection of the military personnel. It wasn't a relationship he had with this man though - just a couple of nights as I understand it. Rodney doesn't trust anyone enough to have a relationship with them. He keeps people at bay."

"I'd noticed," John chuckled. "Okay. Thank you, Carson. You've been very helpful."

"I do my best." Carson flashed him a broad smile. "It's over to you now, Colonel!"


John left the infirmary and made his way back to his office, thinking this through. He was absolutely furious that any of the men on his team had behaved in this way, and decided that they needed to understand the kind of behaviour their commanding officer expected of them. John wasn't a showy man, but he did have certain very firm ideas, and he wasn't afraid of following through on them. He didn't think for a moment that all the men under his command were the same as Bates and his friends, but it was up to him to make it clear to all of them the kind of operation he would be running on Atlantis. In his experience people needed to know where they stood, and John wanted to leave them in no doubt on that score. This might be his first major command, but John had been a leader all his life, and he subscribed to the notion that people took their lead from those in charge, so it was time to let his men know exactly what kind of a man he was. He summoned Major Lorne and asked him to assemble his entire military staff in the punishment room in an hour's time.

"The punishment room, sir?" Lorne raised a questioning eyebrow.

"Yes - the practice room is too small for what I have in mind," John told him, "and the chairs are already laid out in the punishment room so it'll work fine. Get it cleared of the frame and implements - they can be put in the adjacent storage room."

Lorne nodded, and then left, clearly mystified as to John's intentions. John smiled - he liked Lorne but he wasn't sure he could trust him yet, so he'd let the major find out what was going on in an hour's time, like everyone else.

Forty-five minutes later, John collected the equipment he needed from the practice room and carried it along to the punishment room, and then he waited for his men to arrive. He was dressed in practice clothes, fully prepared for what was going to happen next. When the marines started filing through the door, John smiled at them pleasantly, and greeted each man by name, just to make it clear to them that he wasn't some remote commanding officer who would take no interest in them, and also so that they knew they wouldn't be able to hide behind their anonymity. He knew exactly who they were and if they ever screwed up then he'd know who to ream out too.

John waited until they were all seated, and then surveyed them.

"We've had a busy few weeks," he told them. "What with the city shutting down and the wraith attacks. I've had a chance to see you guys in action and I have to tell you that I'm impressed. You're a good team - the best - and I feel privileged to know I've got you guys watching my back when we go out there."

He paused for a moment, and surveyed the room, taking in their faces. That was the softener; the carrot. Now it was time for the stick - literally.

"You guys don't know me very well and I know you've been wondering why the hell an Air Force colonel has been brought in above your own chain of command to run this operation. And the answer to that is - that it's none of your goddamn business." John smiled sweetly, and a little chuckle went around the room. "Now, like I said, you don't know me very well - that's why I've ordered you here, to do a little…military bonding." John smiled again and the men all looked at each other uncertainly, clearly wondering what the hell that meant.

"Okay. Let me lay it on the line. We're out here, in this galaxy, a long way from home, all alone, and the only way we're going to survive is if we pull together and all do things one way - and that way, ladies and gentlemen, is my way. There's no room for any dissent. I'm in charge here, and what I say goes. I'm not an unreasonable man, but I do have some very firm ideas on how the people under my command conduct themselves, and, if any of my special rules are broken, I will happily order you into this room and administer military discipline myself - and I'm sure Major Lorne will also be happy to oblige if I'm unavailable."

John turned, giving that statement a few minutes to sink in, and he went over to the table where he had laid out two sets of fighting batons which had been given to them by the Athosian people in gratitude for helping save them from the Wraith attack on their homeworld, and giving them sanctuary on Atlantis. He picked up one set of the batons.

"I'm not talking about military rules here," he said, as he turned back. "I'm talking about my own personal rules. What can I say? I'm quirky that way." He gave them another little grin, but he noticed they were starting to look a little uneasy, and he could see that they were wondering if they were stuck out here, in the middle of nowhere, with a psychotic commanding officer and nobody above him in the chain of command to appeal to. John did nothing to disabuse them of that notion - he wanted to keep them on edge.

"Now, you've already seen me in action, and I've seen some of you in action too, but I'd like to put a few of you through your paces." John smiled again. "So…I want some volunteers." Nobody ever volunteered in the military so John didn't wait for anyone to step forward. "You, you, you, you, you and you," he said, singling out Bates and the five other men who had been witnesses in the mess hall a few days previously. All of them, as far as John was concerned, were implicated in what had happened with Rodney McKay. "Come here." The men got up, glancing at each other nervously.

John threw a pair of batons at Bates, and then went and got a pair for himself. He was still a relative novice at using these, but he'd had a couple of weeks' tuition from the Athosian woman, Teyla, and that was a couple of weeks more than any of these men had been given so he was confident that he easily outclassed them.

"These," John said, holding up the batons, "are probably unfamiliar weapons to most of you. However, working with them speeds up your reflexes and makes you extremely agile, so you could all benefit from some workout sessions with them. If you want any guidance then ask Teyla. One of the benefits of being in another galaxy is that there are a hell of a lot of new things to be learned…and I'm about to give you your first lesson. Sergeant Bates…come at me please."

Bates hesitated for a moment, then stepped forward, raising his sticks. He narrowed his eyes as he approached, trying to size up the colonel, and then he charged forward, hard, batons flailing. John easily sidestepped him, thwacked the sergeant's hand with one of his own batons, effectively disarming him, and then he swung his other baton low, caught Bates a stinging blow on the legs, tripping him, and, as he fell, he delivered a satisfying swat to Bates's rump with his other stick. Bates lay there, panting and clutching his leg. John gave him a sweet smile and then turned back to his audience.

"Rule number one," John said. "I hate bullying. This, ladies and gentlemen, is a civilian expedition, not a military one. I answer to the head of the civilian team, Lady Weir, and we are mainly here just to protect their collective asses. That's our purpose. They aren't military, and if they ever complain that any of my men have tried to intimidate them, physically or verbally, I will personally take great delight in tanning your hides. Next please."

John threw Bates's batons at the next marine, a big, muscular, blond lad, and he swallowed convulsively and looked around uncertainly. "Now, Corporal!" John snapped and the corporal lumbered forward. John disarmed him with the same ease as he had Bates, and the big corporal went down with a satisfying thump - John made sure to thwack him hard on the backside on his way down.

"Rule number two: most of the guys around here will be smarter than you," John told his rapt audience. "That's just a fact of life. It's nothing personal - get used to it. Now, very smart people don't always act in ways that are easy for the rest of us to understand. That's fine. If you don't understand what one of the scientists wants, or if you think they're placing themselves or the rest of us in danger, then you can come to me, and I'll handle it. Otherwise - remember rule number one. This is their expedition and we're here to protect them, not obstruct them. Next please."

John handed the big corporal's batons to a thin, dark-haired man and beckoned him forwards.

"On the subject of how smart some of these people are - it might interest you to know what Dr Rodney McKay's qualifications are, for example." John grinned, and the dark-haired marine did a fancy little dance and then tried to side-step him. John despatched him without breaking sweat, delivering a hard swat on the man's ass as he went down, just as he'd done with the two previous men. "Dr McKay is Head of Science on this expedition and therefore I think you can assume he's pretty smart. In fact, Dr Beckett described him to me as a genius. "Did you know he graduated from MIT summa cum laude with a double major in math and physics when he was only seventeen?” John gazed at his audience dispassionately, recalling the facts he'd memorised from McKay's file. "Since then he's earned advanced degrees in mechanical engineering, applied mathematics, astronomy and astrophysics from the University of Toronto and Cal Tech. He also happens to be extremely important to this expedition as he's the only one who fully understands how the Ancient technology works."

John gave them a few seconds to digest that information, because he wanted them to be in no doubt at all on the subject of Dr McKay. There wasn't a whole lot he could do for the Head of science to make up for what he'd endured that morning, but he could do *this*, if nothing else. Then he gestured to the next marine in line to come forwards.

"Rule number three: integrity. We might be a long way from home, but I still expect you to behave with the same standards of behaviour and integrity that I'd demand from you on Earth."

John feinted to the right, then took out his new opponent with a single flick of his wrist to the left. The man landed in a heap on the floor and John swatted him on his ass on his way down.

"Rule number four: obey me, take your lead from me, try and impress me - and we'll get along just fine." John gave another sweet smile as he called forth the next marine.

"Rule number five: I'm in charge. That's it. I'm your bottom line, ladies and gentlemen. Piss me off and by god you'll know it."

John saw off the remaining marines in lightning quick time, as if to illustrate that point, and then threw the batons back at Bates once more.

"Again, sir?" Bates asked, looking seriously pissed off.

"Oh yes, Sergeant Bates. Seven more times to be precise," John told him with another of those bright smiles. Bates glowered at him but John was sure that the symbolism of the number wasn't lost on him. John took on each of those six marines another seven times, and on each occasion they landed in a heap on the floor with the sting of his baton smarting on their asses, legs, or hands. When he'd finally finished with his object lesson, they were all looking dejected and decidedly the worse for wear. His audience was also looking subdued, clearly processing the knowledge that their new commander might not be psychotic, but he sure as hell was a hard ass. John didn't think there was any one of them who didn't know what the session with the batons had been about, and that was all to the good as far as he was concerned. When he'd finished wiping the floor with Bates and his cronies, John swung his batons up, and turned back to his audience.

"Well, this has been great, ladies and gentlemen. I've appreciated having the chance for you to get to know me a little bit better. Did anyone have any questions?"

Bates raised his hand, and John's eyes flickered over him in cool distaste.

"Good," he said, ignoring the man. "Now, if any one of you feels that maybe he's lost my good opinion, I would like you to know that I'm sure you can win it back, with lots of hard work and application and by following those rules of mine. That's all." And so saying, he swept out of the room.

End of Part One

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Part Two