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Author's Chapter Notes: AN: Thanks are due to Elgin, who helped me refine some of my ideas regarding how John can take command of Atlantis given his lack of pre-existing experience with Earth's military, as well as helping me actually write this meeting with the IOA

Looking at the infirmary around him as he sat on the side of his bed, standard tests completed and currently alone in the room, John wondered if it was normal to feel so strange after arriving back on your home planet for the first time in over two decades.

OK, he'd been through a lot since he'd last been on Earth, forced to grow up faster than he should have done and take on responsibilities that nobody would have ever forced upon a teenager under conventional circumstances, but it was still the place where he'd been born; shouldn't he feel a bit more… connected… to this place?

That said, it wasn't hard to work out why he wasn't feeling particularly connected to the planet; for the last two decades, he'd been thinking of Atlantis as his home first and foremost, and even if he'd moved on to accommodate Elizabeth's return to his life, he wasn't yet ready to admit that he would consider anywhere home if she was there…

He stopped that thought before it could go further; things were complicated enough here without having to worry about him admitting to… that. He knew enough about the situation on Earth to know that his potential position as Atlantis's new military commander was already precarious even with General O'Neill and Mr Woolsey backing up Elizabeth's recommendation of him for the position; the last thing he wanted was to give the IOA review board potential ammunition to declare him unfit for duty due to his relationship clouding his judgement or anything like that…

"So," a familiar voice said, John looking up as the speaker walked into the room, "all it took to get you to work with us was offering you a job?"

"Colonel Sumner," John said, nodding politely at the older man, declining to answer his query.

"John Sheppard," Sumner replied, grimly looking him over for a moment before he raised a sceptical eyebrow. "Or is that even your real name?"

"It's my name," John confirmed, nodding back at Sumner; he might not have to work with the guy any more, but that didn't mean that he was going to be completely dismissive towards everything he had to say. "I came from Earth, and ended up in Atlantis through a mix-up involving an Ancient teleportation system and time travel; didn't you read the report?"

"I read it; I just have to wonder about the events described," Sumner said, still looking at John in a pointed manner.

"If you think this was always my plan, it wasn't," John said; the dynamic that he and Elizabeth were planning to propose to the IOA might be more complicated than what he was describing to Sumner, but he wanted to stick to the essential points right now rather than get in a debate with the guy. "I never set out to replace you; Elizabeth offered me the position, I accepted, and that's it."

"'That's it'?" Sumner repeated, looking grimly at him. "Do you really think that you can lead my men against the Wraith with just a few recommendations behind you? You have no experience of working with others-"

"I've studied and adapted Ancient tactics from their database for the past couple of decades, Colonel; considering that those plans were drawn up to be used by a group, I think I can accommodate working with other people," John said, staring firmly at his predecessor (He hadn't intended to think it, but now that the word was out there, he found he rather liked it). "I acknowledge my limitations, but I'm not incompetent; I have a plan, and I can make this work."

"You have no training-" Sumner began.

"He has no training that you would recognise, Colonel Sumner; that does not mean that he has no training," a deep, formal voice suddenly said from off to the side of the infirmary, prompting both men to turn and look at the speaker; a tall, dark-skinned man with short dark hair and a distinctive golden tattoo on his forehead. "I would suggest that you avoid dismissing someone as effective because they have not experienced what you have."

Looking at the man in frustration for a moment, Sumner turned and walked away, leaving the man to enter the infirmary.

"Teal'c?" John said, looking at the tall man in surprise; he might not have met the guy, but the description he'd received from Elizabeth during their first meeting wasn't one that you could confuse for someone else.

"Indeed," the Jaffa said, nodding at the masked man before him. "It is an honour to meet you, John Sheppard… or would you prefer for me to refer to you as 'the Phantom'?"

"Hey, you're part of SG-1; after all you did for this galaxy, from what I've heard, you can pretty much call me what you want," John said, smiling thankfully at the Jaffa before he noticed four other people now walking into the room behind Teal'c.

It had been months since he'd seen them last, but SG-1's visit to Atlantis wasn't something he'd have been likely to forget; even if Morgan Le Fay hadn't made a brief appearance at the time, he'd heard enough of Elizabeth's stories about them to realise what they meant to this galaxy.

"Well, if everything we've been hearing about you these last few years is true, it sounds like you've had some experience in that area yourself," Lieutenant Colonel Cameron Mitchell said, smiling in approval at the masked man.

"I didn't exactly save anything; I just slowed the Wraith down a bit…" John said with a self-deprecating shrug.

"You slowed them down without any actual training aside from whatever you picked up since you got there, and destroyed at least five of those hive-ship things in the process; makes you a hero by any definition far as I'm concerned," Mitchell said, grinning at him.

"And you've certainly come a long way since you got there, if what we've heard in those latest reports is true," Vala Mal Doran said, looking him over with a grin before her gaze settled on his mask. "A shame about that thing, of course, but I suppose your reasons make sense; no point saving the day if you're going to scare everyone off."

"They weren't exactly scared; 'hostile' is the term I'd use," John said, trying not to think too much about the smile Vala was giving him; even if it was a change to have someone… looking at him like that… his encounter with Chaya had been proof that he would always feel uncomfortable in that kind of position unless it was with Elizabeth, to say nothing of being unfair to anyone else involved.

"Still, your insight into the Ancients must be absolutely fascinating," Daniel said, smiling encouragingly at him. "I mean, you've been living and training using the same resources they would have had access to all these years ago, without too many of our own cultural preconceptions to tie you down…"

John honestly tried to pay attention, but as the archaeologist went on, he was just left feeling increasingly uncomfortable as he took in the sheer scale of the archaeologist's knowledge and passion for anything relating to Ancient history, and found his own wanting. He'd done some background reading to learn more about the Ancients themselves, but he'd only focused on what he needed to know to ensue he didn't blow up Atlantis or stumble into something the Ancients had left alone for a reason; this guy read up on everything.

He'd done what he could to learn more about the city, but some parts of Ancient history just hadn't been that interesting to him in the end; he'd always been more focused on anything Wraith-related rather than their general histories…

"Anyway," he said, taking advantage of Doctor Jackson having apparently run out of questions (or possibly just breath) as he looked over the group gathered around him, "I appreciate your support, but we have to face the facts; whatever you said to Colonel Sumner, I really don't have training in this kind of thing."

"But-" Vala began.

"No, he's right," Mitchell said, looking apologetically at the other man. "I mean, I can get you wanting to get Sumner out of the city, and I'm fully aware that you're good at what you do, but you have to face facts; tactical differences aside, only some of the city's military contingent are going to completely accept you as a replacement…"

"Which is why I'm not going to be the only leader," John replied.

"Excuse me?" Sam said, looking at him in surprise.

"We wanted to make sure that Sumner understood that he wasn't going to be welcome back, but I acknowledge that I'm not qualified to take command of such a large operation despite my superior experience with the Wraith," John explained. "General O'Neill and Mr Woolsey's recommendations will smooth the process along- they can vouch for my capabilities in the field- even without everything you've learned of my track record against the Wraith, and I already have a candidate in mind for my co-leader from Atlantis's pre-existing military division."

"Sounds… workable," Mitchell said, nodding in contemplation as he looked thoughtfully at John. "Bit unorthodox, of course, but we've got a precedent for that kind of thing with Teal'c and Vala here on Earth, and there's all the Athosians the expedition's been working with in Atlantis; what you're proposing is more… definite… but you can still argue that other people have tried it…"

"Exactly; I'm not defying the way you do things, I'm just asking to jump over a few of the usual procedural restrictions in the face of a uniquely complicated situation," John said, nodding in agreement at Mitchell's assessment. "Considering that I've been keeping your expedition safe for the last few years alone, it's not like I'm asking anyone to take a leap of faith; you all know what I can do, and I'm just asking for the right to make it official."

He paused for a moment as he looked at the group around him once again, smiling slightly as he noticed Sam and Mitchell's sceptical expressions. "Besides, I don't blame you for doubting me; I was actually going to ask to meet with you if you hadn't come here yourselves."

"Why?" Sam asked.

"I want a crash course in Earth military tactics," John said firmly.

"Excuse me?" Vala said, looking at him in surprise. "You just said-"

"I've saved Atlantis by doing my own thing; if I'm working with other people now, I need to have a better idea of how to incorporate their training and tactics into my plans," John clarified. "General O'Neill's obviously busy, and I'm naturally not exactly in a position to ask Sumner for his own insights, but after everything you've all dealt with over the years, I think it's safe to say that if there's anything you can't teach me, it isn't worth knowing."

For a moment, as the five members of SG-1 exchanged glances with each other, John worried that he'd asked for too much from them- it wasn't like they didn't have other things to occupy their time at the moment, after all- but then Mitchell shrugged and turned back to look at him with a casual smile.

"What the hell?" he said, looking back at John with a smile. "Considering how important Atlantis is, I think we can spare some time to give you a crash course."

As he sat opposite the group of IOA officials assigned to determine his suitability for the position of military leader, John wished that he felt more prepared for this meeting.

He'd spent the last few hours talking with SG-1 about everything that he could think of that might come up in an interview, discussing what he already knew how to do and demonstrating what he was capable of in terms of hand-to-hand combat and marksmanship (His aim with more conventional Earth weapons was slightly less efficient than it could have been due to his lack of experience with them, but it was enough to get the job done, and his combat style tended to emphasise speed and wearing down the opponent since his regular foes were so much stronger than him), and he was currently accompanied by both Sam Carter and Cam Mitchell who were ready to step in if it seemed like he needed it, but there was still only so much they could do at this point.

The politics of it were all a headache, but so long as nobody outside China seemed interested in going along with Shen's suggestion that a Chinese officer would be a suitable candidate as Sumner's replacement, John felt that he could win over most of these guys…

"Mr Sheppard," Woolsey said as he sat directly opposite John on the other side of the long table that had been set up for this meeting with the IOA, the American representative looking solemnly at the masked man, "my colleagues and I have been conferring about Doctor Weir's request to appoint you the head of Atlantis's military division, and… to put it bluntly, we have our doubts."

"Doctor Weir and I were aware that you would, Mr Woolsey," John said, nodding at the older man. "We weren't expecting automatic acceptance of our proposal, and you'd be foolish if you gave it; what we are expecting is that you hear me out and give me a reasonable chance to prove myself, rather than dismiss me completely because I'm not what you'd expect."

"Indeed?" the British representative- a Mr Chapman, if John recalled some of the information he'd picked up correctly- said, looking curiously at the masked man. "And you expect us to agree with your proposal?"

"I hope you will, anyway," John said, nodding politely at the other man. "I think I've proven through my assistance to Atlantis over the years that I'm not your enemy-"

"Which brings up a point I feel should be addressed," Shen said, looking pointedly at him. "Your… unusual… history has been explained, but I feel obligated to ask; considering that you have been away from Earth for some time, why should we believe that your interests are aligned with ours where Atlantis in particular and Earth in general are concerned?"

"The fact that I didn't just come back here as soon as I could and draw your attention to what was out there?" John countered, looking firmly at the Chinese woman; if she was hoping to provoke him by questioning his loyalty, he wouldn't give her the satisfaction. "You've achieved so much in the decade since you first opened the Stargate, but all of that was mainly possible with what you'd learned about the universe before the first trip to Abydos. If I'd come back, Earth would have gone out there without access to who knows how many of the scientific breakthroughs you've needed to survive out there, and you probably wouldn't have had access to all of the staff you've employed since you actually started the project-"

"In other words, you didn't come back because you thought you knew best," Shen said, staring at John in a manner that seemed neutral until you realised the intensity of the stare that you were receiving. "You may have been able to save lives by warning us-"

"I would have saved Earth and damned the universe," John said firmly; that attitude might not win points with the traditionally 'Earth-first' IOA, but it was an honest assessment of the situation and he'd be damned if he didn't make the point. "Doctor Weir was only able to tell me the basic essentials of what the Stargate program has accomplished during its existence, but that was enough for me to know that you were all needed out there; if I'd come back, I would have been putting Earth at risk if I'd been encouraging you to go out there, or leave other worlds in danger or under continued oppression if you'd decided to cut off the Stargate program. People have died, but I didn't have time to ask Elizabeth for more information about what was going to happen here; I would have been of little real aid to you here, but by staying where I was I was able to preserve Atlantis and deal with the Wraith for you."

"Well said!" the Russian delegate said- the man's name was apparently Cherednik, and he was a new addition to the board, from what John had heard- grinning in approval at John in an exaggerated manner that John didn't entirely trust; the slightly overweight guy just seemed to be making too much effort to be likeable for John to feel comfortable trusting him. "I for one can affirm that we are completely grateful for your dedication to Earth's security, Phantom-"

"John," John interjected.

"Pardon?" Chapman said, looking at the masked man inquiringly.

"I'll retain the name 'Phantom' for my activities in Pegasus, but I would prefer to be known as John," John explained. "Recent events have left me… dissatisfied with the Ancients' apparent approach to their responsibilities in Pegasus; I would prefer not to be associated with them any further than I have to be."

"Ah… I see," Cherednik said, nodding briefly in understanding before he continued. "Regardless, I must confirm that we are very much appreciative of your decision, John Sheppard; while we regret that you were unable to come back to Earth sooner, I can assure you that your motives are fully understood and appreciated, and we welcome any input you have to offer regarding your experience with Ancient technology."

"Thank you," John said, making a mental note to keep an eye on that man; he might leave politics to Elizabeth, but he'd heard enough stories over the years to know that the Russians had a few issues with the Stargate program being a purely American-run institution.

"And of course," Cherednik continued, looking at John with a warm smile that suddenly reminded John of Lucius trying to curry favour with Elizabeth, "your sterling reputation can guarantee you our full support in your request to take command of Atlantis-"

"Command of its military division only, General," John said (A quick glance at the man's ranking insignia confirmed the rank; at least Carter and Mitchell had been able to cover hat much). "As I said before, I have full faith in Doctor Weir's abilities as a diplomat and general coordinator."

"Will you be effecting many changes in how the city is currently run on a daily basis?" Woolsey asked.

"I might encourage people to interact with their teammates more off-mission, but otherwise I don't think so," John replied, hoping he'd phrased this part appropriately; he wanted to make it clear that he had plans, but at the same time he didn't want to act like he knew better than the people who were in control already. "Sumner was very efficient at coordinating his staff throughout the city, but he believed in maintaining professional detachment, whereas I always felt that, if I was going to work with anyone, I'd want them to know they could count on me as more than another gun when things get ugly…"

He shrugged slightly. "I'm not condemning Sumner's methods; I'm just saying that I'd do that differently."

"And we'd probably have to deal with those changes no matter who we appointed, wouldn't we?" Cherednik said, looking over at the other delegates.

"Quite," Chen said, even as the slight glare she gave John at least hinted that she doubted that he was the appropriate candidate for this task.

"Let's focus on the essential details, shall we?" Chapman said, shooting a brief glare at the Russian delegate before he turned his attention back to the masked man opposite him. "Regardless of your unorthodox arrival on Atlantis, John Sheppard, do you feel that you can fulfil the duties of an SG expedition leader with diligence, integrity, and respect for those in authority over you?"

"Yes," John said, leaving out his private musings that he would obey orders from Elizabeth or General O'Neill over anyone else; they were probably all already aware of that particular fact, but he wouldn't win himself any favours by making it explicit.

"That's good enough for me, then," Cherednik said, grinning around the table at his colleagues.

"I second that recommendation," Woolsey said, nodding briefly at John as he spoke; evidently, even if John and the rest of the Atlantis staff had used him to trick the Asurans, he accepted that it had been for the right reasons.

"Talking of your contact with other SG teams," Chapman said, indicating Carter and Mitchell as they sat on either side of the masked man, "shall I assume that SG-1's presence here means that you have their approval?"

"He's asked us for help dealing with the weak links in his training and experience," Mitchell clarified, "Guy knows he's good, but he's also smart enough to know what he needs working on; until he goes back to Atlantis, he's asked us to train him in tactics when we have the time."

"You requested training from SG-1?" Chapman said, looking at John in cautious approval.

"I did," John replied.

"Well," Chapman said, sitting back in his chair with a slight smile on his face at the thought, "considering what I've seen SG-1 achieve in the past, I feel safe saying that you will have a very… interesting way of doing things after learning from them, to say the least."

"Which brings up another point I wish to discuss," Shen said, looking at John in her usual pointed manner. "While you have demonstrated a defiance of authority in our past interactions with you, you have made it clear that you will accept orders from Doctor Weir despite her past errors in judgement-"

"If you've read General O'Neill's report on my activities in the Pegasus Galaxy, you will be aware that an alternate version of Doctor Weir had a prominent role in my experience," John pointed out, trying to keep his manner direct without being too blunt. "I was young when I met her, but I learned a great deal from her, and therefore knew from experience that she could be counted on as a leader."

"From one meeting over two decades ago?" Shen said, looking sceptically at him.

"A single meeting that taught me what I needed to know to survive for those two decades," John retorted nonchalantly. "She was able to instruct me in how to stay alive all those years ago, and I would be equally willing to take General O'Neill's orders if he and I were ever working together, because I know their skills and like them as people."

"You disapprove of Colonel Sumner's skills?" Woolsey asked.

"I disagree with some of his opinions of how to do things; that's not the same thing," John pointed out.

"In any case, John Sheppard's ability to lead or take orders is not in question here," Chapman said, looking firmly at the masked man. "General O'Neill, Mr Woolsey, and Doctor Weir have all vouched for your abilities in combat, but I will confess to some apprehension about your ability to cope in a situation where you have to make the hard choices."

"The hard choices?" John repeated.

"As much as we would like to imagine otherwise, there may come a time when you have to choose between letting someone die and putting Atlantis at risk," Chapman said, looking solemnly at him. "Can you do that?"

"I have already," John said.

"You did?" Shen asked, looking at him in surprise. "When?"

"I gave Doctor Weir a report on it before I came here," John replied (Which was totally true; he had just neglected to mention how long it had been since he gave her the aforementioned report). "When I was briefly held captive by the Wraith you know as Michael Kenmore, I discovered Lieutenant Ford being held prisoner while Michael subjected him to various experiments to mutate him into a hive-ship with a Wraith pathogen; when it became clear that there was no way to stop the mutation, I decapitated Lieutenant Ford on his request."

The matter-of-fact way in which he delivered that report may have disturbed some of the delegates- that was the disadvantage of dealing with civilian oversight; they wouldn't really get why things had to be done that way- but it seemed as though he'd made his point.

"Well," Shen said at last, briefly losing her grip on her pen as she turned back to her notes, "even assuming we… accept that… as an example, we do have… other issues… regarding your ignorance of contemporary military training and techniques-"

"Which is why I'll be working with someone else," the masked man clarified. "He'll handle the finer details of coordinating with the staff, as well as instructing me in any Earth tactics or pre-existing stratagems that may be useful for me to know, while I come up with the plans and use my knowledge of the Wraith to its fullest extent."

"And we're training him as well," Mitchell put in. "Can't promise we'll turn him into an academy graduate in a matter of hours, but we'll make sure he has some idea what he's doing."

"Of course," the French delegate said, nodding briefly at Mitchell before looking curiously at John. "Will you be asking others for training?"

"I will generally defer to SG-1's recommendation in this manner, but if they feel that someone can be trusted to teach me something useful, I will accept any input offered," John confirmed; he was surprised that this was the first question the man had asked, but considering what Elizabeth had told him about this man preferring to watch rather than force his view on the group, he supposed it made sense. "However, I will be making my own choice for my second-in-command; I have some possible candidates in mind from Atlantis's current staff, but I'll get back to you when the time comes to make my choice and give you the chance to make a case for any alternatives."

With that said, he sat back and looked around the table. "So, ladies and gentlemen, do you have any further questions?"

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