Commander's Office, Atlantis
New Lantea, M35-117
Pegasus Galaxy

Jack was settled on Carter's surprisingly comfortable desk chair and had only just booted up her work laptop to tie up some loose ends when Sheppard knocked on the door of the office. "Come on in," he said, beckoning the younger man inside with a wave of his hand. "What can I do for you, Colonel?"

"General," Sheppard greeted before entering the room. "I was looking for you, Sir. I had actually already stopped by your quarters and the mess hall until I heard you were here."

He frowned and focused his attention on the dark-haired officer. "So, what's this about?"

"Chuck told me there's an outgoing wormhole to Midway Station scheduled for tomorrow morning."

"That's right," Jack said slowly, wondering what was up with all the questions. Had Carter already told her 2IC about her going back to Earth or was he simply curious about the 'gate's activity? "What about it?"

Sheppard shifted on his feet and seemed to contemplate his answer. "I was just wondering why, Sir. I mean, it's not our regular time to check in with Earth and Chuck said you had specifically said Midway and not the macro to dial the SGC via Midway. So, I figured it had to be something important and the only thing I could come up with was if you were sending people back, which usually only happens to those on leave but I don't believe there's anyone scheduled for some regular or medical leave Earth-side."

"Ah," he muttered. "Well, there's Carter…"

"You're sending Colonel Carter back to Earth? Sir?"

Jack shook his head and tried to explain. "No… well, yes. But only because she's got a broken leg and needs to recuperate. A combat zone like Atlantis is not the place for someone to take medical leave of a few weeks."

Sheppard appeared to be a bit upset about that if the scowl on his face was any indication. "Does she know? Because she hasn't mentioned anything to me yet."

"She knows, I told her yesterday," he replied. Then, thinking back to the time they'd spent together on the pier, he shrugged. "Well, she kinda came to the conclusion on her own and I confirmed it."

"So you'll be staying here for the next few weeks, General?"

Smirking, Jack wondered if there was a bit of panic in Sheppard's eyes at the prospect. "Nah, I'm gonna escort Carter back," he said.

"So, you'll be coming back then?"

He grinned, trying to imagine the shock on the team leader's face when he'd realize who exactly was going to be in command of Atlantis for the next few weeks. "No, I need to get back to Earth soon too, so I figured I might as well combine it with Carter's trip back."

The dark-haired flyboy looked thoroughly confused – which pleased Jack immensely – and it took him a moment to come up with his next question. "Then who'll be in charge here and when are they going to show up? Is it someone from the IOA, or Woolsey himself maybe?"

"Nope," Jack said, amused by the obvious distaste in Sheppard's voice. "I told you when I arrived that the IOA eventually agreed with me on the military command thing, so no Woolsey or someone else from the IOA."

"Then who, Sir?"

"Some flyboy with a somewhat questionable record according to some," he replied. "You know, disobeying direct orders, unsanctioned ops, a black mark… but people who've worked with him seem to respect him."

Sheppard cleared his throat awkwardly and briefly glanced at the floor. "Anyone I know, Sir?"

"Actually, I believe you know him quite well."

"Is that so?"

Jack nodded in affirmation and leaned back in his chair, folding his hands behind his head. "Yep. Elizabeth relied on you to handle all things military and Carter certainly seems to trust you or you wouldn't be her 2IC."

The Lieutenant Colonel quirked a brief smile at the remark of how the two commanders of Atlantis – previous and current – trusted his capabilities before his expression turned into a grimace. "Wait, are you saying I am supposed to take over until Colonel Carter returns in six weeks?"

"Well," he sighed, "the six weeks is really more of an estimate. It depends on how well her leg is healing and she may need another type of cast or simply physical therapy for a little while afterwards, so it could even be two months or longer."

"But-"

Jack held up his hand to forestall his protest. "Ack! Don't argue with me about this, unless you'd rather have Woolsey boss you around for the next few weeks?"

Sheppard glared at him and suddenly appeared a bit restless. "Of course I don't want Woolsey here but I saw what the IOA did with Elizabeth and sometimes still tries with Colonel Carter – all the politics and red tape is really not my style, Sir."

"That may very well be but you can't have it both ways, Colonel; being team leader of the flagship team and having certain privileges as the base commander's 2IC without actually doing the hard stuff like taking command when your CO is unable to do so. I know you also like your independence and you don't want to be stuck behind a desk or responsible for everyone in this city but in a way you already are as the most senior officer next to Carter. Simply put, Sheppard, with your position come certain responsibilities-"

"I know, Si-"

Jack grunted at the interruption and slammed his hand on the desk. "You can't have your cake and eat it too, Colonel. Remember our little talk prior to your diplomatic mission to M5V-801?"

The Lieutenant Colonel grimaced, nodding slowly. "Yes Sir."

"Good, because this is one of those things that I – and Carter, too – don't really trust anyone else with at the moment. Right now, I think you're the best man for the job and I think we both know Carter is grooming you for command anyway, regardless of what you want because she also doesn't want to see some IOA shrub taking over when she's reassigned in the future. As her 2IC you've got to have her six and step in for her, or things-"

"Will go to hell in a handbasket," he finished for him.

"Exactly!" Jack exclaimed, pleased that they seemed to be on the same wavelength here. "You know this city better than anyone else of our expedition and you're the best we've got to handle the chair or even the jumpers… but if you don't feel like you're up to doing the difficult part of the job I'm sure we can find you a nice and easy reassignment. Maybe back to Antarctica, seeing as how much you liked it there. We'd have to find someone else to lead your team but I'm sure Ronon and Teyla would understand, or at least pretend to as most aliens tend to think we humans are a bit weird anyway. McKay… well, he always complains no matter what but he'll adapt or be sent back to Earth too and I think we both know he wouldn't want that, so he'll play ball eventually. It's his new team leader I'm more worried abo-"

Sheppard threw up his hands in a frustrated gesture and interrupted him again. "Okay, I get it, Sir."

"Good," he said curtly. "In that case, you have until the scheduled wormhole to Midway Station. If you haven't made up your mind about whether or not you belong here and are capable of taking the responsibilities that come with your position, then you might as well make go through the 'gate yourself and I'll wait here for Woolsey to show up. Who knows, you two might be able to share the better part of that twenty-four-hour quarantine together on Midway."

"Gee, thank you, General."

Jack smirked at him before focusing on the laptop in front of him again. "Glad we got that settled then, Colonel. Now just go about your business while I do important commander stuff," he said, making a shooing motion with his hand. When he heard footsteps moving away Jack looked up again and stopped the man when he neared the door. "Oh and if you decide you're not capable or worthy of this command then please let me know in time; I'd hate to have to unpack all my things again in the morning."

"Will do, Sir." Sheppard threw him a lazy salute before exiting the office.

He watched him go and briefly wondered how long it would take the flyboy to tell him he was ready to man up and take over for Carter. Jack doubted it would take Sheppard long as everyone knew the man belonged here on Atlantis and was more in his element here than he'd ever be in Antarctica or whichever continent on Earth. It was just a shame that he let his distaste for politics and red tape get in the way of fulfilling his potential, although Jack also knew the dark-haired Lieutenant Colonel wasn't ready for full command yet, but that's why he was Carter's 2IC – to learn along the way.

Besides, if Sheppard got through the next six weeks or so relatively unscathed then maybe Jack could welcome his wife a bit more on Earth, as Carter would then feel more comfortable taking longer periods of leave to come home…


Carter's Quarters, Atlantis
New Lantea, M35-117
Pegasus Galaxy

Sam was standing on her balcony and drinking in the sight of the city, the ocean and the feel of the alien sun on her face when she heard the distinct sound indicating someone was at her door. Her crutches were next to her, leaning against the balustrade but since she hadn't locked the door she simply waited for whoever it was to enter her quarters. She wasn't surprised to see John Sheppard cautiously sticking his head in because she knew Jack had talked to him yesterday about him replacing her during her recovery. "John, come on in."

"Colonel," he replied upon spotting her. With a small smile he entered the room and headed her way after casting a glance at the bag on her bed. "All packed?"

"You betcha." She leaned back against the balustrade and waited for him to join her. "General O'Neill and I have to leave for Midway soon, so…"

John squinted as he stepped into the sunlight. "Six weeks, right?"

Canting her head Sam grinned at him. "Thereabouts."

"Ah."

"Think you can fill in for me?"

He grimaced, his eyes darting to her cast leg before they came up to her face again. "General O'Neill already gave me the talk yesterday."

Sam chuckled softly at his discomfort. "I know, he told me. And he may have mentioned something about throwing you through the 'gate to Midway Station himself if you refused."

That got a snicker out of him. "I don't doubt it!"

"You'll do it then?"

"Well, if it's between me and Woolsey…"

Reaching out Sam touched his arm. "John, there's a reason Elizabeth wanted you on this expedition and why General O'Neill approved it. If neither of them thought you were fit to lead the military contingent of the Atlantis Expedition after Colonel Sumner was lost then they would have gotten someone else to replace him. If you hadn't done such a great job here you wouldn't be my 2IC, either," she added.

He shook his head and ran a hand through his hair, smiling slightly. "Yeah, General O'Neill mentioned something like that, too. He also said something about you grooming me for command…"

"You can't stay in the field forever," she said, shrugging. "Trust me."

"Maybe but … flying a desk?"

Sam rolled her eyes indulgently, mildly amused at his whining tone that sounded oddly similar to Jack's when the subject came up. "You're in your late thirties, John. How much longer do you think you can do fieldwork? If it's not your physique or medical problems in a couple of years then you'll likely be pulled for fear of psychological damage after all the brain-probing and life-force-sucking encounters with aliens-"

Her 2IC frowned and interrupted her cheekily. "I thought this was supposed to be something like a pep talk for me to step in while you're on leave but now it's just getting depressing, Colonel."

"I'm just saying," she said, smiling, "provided that you'll continue to be a good team leader and also do your duties as a second-in-command regardless of your distaste for politics and such you'll no doubt make it to full bird in a couple of years."

"But…?"

Shrugging, she turned around and leaned on the railing with her forearms. "But after a few more years there's no place for you in the field. Trust me, there's only so much abuse your body and mind can take."

John mirrored her pose, with just a few inches between their shoulders but didn't say anything until her eyes landed on him. "Is that what happened to you?"

"No, after eight years on SG-1 I requested a transfer," she explained. "After all the things I'd seen and experienced… I needed something a bit more normal and after losing so many friends I felt my luck was going to run out sooner or later. There was a lot going on in my personal life too and I just needed some time to breathe and reorient myself."

"Your dad died, right?" He asked cautiously after a moment of silence, his voice soft and tone somber.

Sam smiled wanly and nodded, knowing it was a sensitive subject for him too as he had just lost his own father recently. "Yes, among other things. Cassandra was also going through a rough time at university and Nevada is a heck of a lot closer to UCLA than Colorado Springs, not to mention how working at Area 51 gave me more flexibility and regular hours to be there for her."

"The girl from the photo in your office."

"Yes, she was an alien orphan our CMO – Janet Fraiser – had adopted in the first year of the Program…"

John nodded, probably recalling some things he'd heard through the grapevine from people who'd worked at the SGC before Atlantis. "She died, right? A couple of years ago."

"Almost four years ago," she confirmed. "Janet was my best friend and the only parent Cassandra had at that time, so after her death Cassie moved in with me since it would only be a couple of months until she would be off to college. Anyway," Sam said, shaking off the memory and pain she still felt at the mention of Janet. "I went to Area 51 because I wanted to. After eight years of fighting a galactic war and watching too many people die it was a nice change of pace."

He shuddered and glanced up at the sky, as if he could see beyond it into space. "I can imagine." Then he canted his head and glanced at her curiously. "Still, you went back."

"My expertise on certain technology my department at Area 51 had created was needed in the war against the Ori and so I was temporarily reassigned to the SGC," she explained. In a way she had been happy to go back and see her friends again but at the same time she hadn't wanted to go back to fight the Ori, especially not when she and Jack had finally gotten romantically involved and the 'temporary' assignment placed her right back in his chain of command. "Of course, things never go as planned and temporary became permanent." Kind of like her relationship with Jack, but in a good way.

"And then you ended up here," John concluded.

Sam nodded slowly, remembering how she had been simultaneously excited and terrified of taking command of the alien city. Surprisingly, Jack had been the one to persuade her to take it and he'd used similar arguments as the ones she was sharing with John now; how much longer could she survive in the field and what would be next if she refused Atlantis? Area 51 perhaps but she had already been there, done that and was kind of over it.

"You've done a great job so far," her 2IC said, breaking the silence.

"Thank you."

John shrugged as if it was nothing and then casually pointed at her cast. "Well, except for the leg."

She chuckled, shaking her head. "Yes, I know. You're not the first person to point that out."

"General O'Neill?" He grinned when she nodded in affirmation, obviously pleased he'd guessed correctly. "Any regrets about taking the job?"

"Climbing on those rickety crates comes close but overall, no." Sam said firmly. Then again, if she hadn't fallen down and broken her leg Jack wouldn't be here and she would have to go without seeing her husband in the flesh for a couple of more weeks, so all in all it wasn't that bad. Spending the next six weeks or so with Jack in DC certainly wasn't a punishment, as long as she knew her command was in good hands. "You?"

"Colonel?"

At his confused tone she waved her hand around, trying to encompass the alien city. "Do you have any regrets about taking the job? I know you weren't too keen on it when Elizabeth first made you the offer."

His eyebrows shot up and he seemed genuinely surprised. "You do?"

"I heard about your conversation with General O'Neill," she replied, recalling how Jack had told her about their first meeting. "In the helicopter," she added.

"Ah yes, he was very, um," he grinned, "succinct. He gave me only until we reached McMurdo to decide whether I wanted to join Elizabeth's expedition."

"He's like that," she confirmed. "Very, um-"

"Unconventional for a two star," John supplied. "But in a good way, of course."

Sam smiled at the quick addition, knowing Jack would be pleased to learn people thought he was 'unconventional' since he'd never really enjoyed becoming 'the Man' and even less so when he'd been more or less forced to take over HWS from General Hammond. "That was over three years ago," she reminded her 2IC. "No regrets?"

He shook his head, a cocky smile on his face. "Nah, the General was right; anyone who doesn't want to go through the Stargate is crazy. Not to mention Teyla and Ronon… even Rodney is okay, I guess."

"And what about the next five or ten years?" She asked, raising an eyebrow at him. "Do you think you four will still be alive and working as a team? If you survive you'll eventually be pulled from the field; the back, knees and brain can take only so much and the brass will probably want you to remain alive because of your ATA gene and how adept you are with the chair and other Ancient technology."

"You're not pulling any punches, are you, Colonel?" He asked, running a hand through his hair.

"John," Sam said, "you're a big boy and you don't need me coddling you. What you do need is a future, preferably one in which you're still alive, on active duty and continuing to keep Atlantis safe. You're the best choice for my replacement because of various reasons, like being able to handle Ancient technology innately and work with military, aliens and civilians alike."

He chuckled mirthlessly and looked out over the city. "So, basically I'm the best man for the job and I should be looking at the bigger picture since it's not just about me anymore. That sounds awfully familiar."

"Really?"

"General O'Neill may have said something along those lines as well," John said.

Reaching out she briefly touched his shoulder in encouragement. "You should listen to him, John."

"He's got quite the reputation," he admitted.

Sam nodded in agreement, knowing just how true that statement was. Jack might not always play by the rules and he didn't blindly follow orders, but in the words of General Hammond there simply wasn't a rulebook for the kind of work they did. Still, Jack was respected by the men and women he'd served with, that had been proven time and again at the SGC and even all the politicians and diplomats he had to work with these days seemed to respect – or at least fear – him. "You remind me of him in some ways," she said, grinning. "You two certainly share the same aversion to paperwork, politicians and anything diplomatic."

John chuckled softly in reply. "Yeah, he may have mentioned something about intensely disliking his job but basically putting up with it for the greater good, until someone he trusts is ready to take over for him and he can retire."

"Sounds like him."

"Elizabeth told me something similar a long time ago," he said after a minute or two of silence. "About my service record and gut instinct resembling that of General O'Neill."

His wistful tone got Sam's attention and the faraway look in his eyes tugged at her heartstrings. She observed him for a moment and came to the conclusion that he was perhaps even more like Jack than either of them had realized. Smiling gently she placed her hand on his where it was grasping the balustrade tightly. "You miss her."

Slowly, John looked up and his eyes found hers. Sadness and grief flashed in his. "Yeah, I do."

"You two…"

"I cared about her," he admitted softly, looking down. "I don't know, maybe in time…"

Sam squeezed his hand before pulling hers back, sensing this was private and really none of her business. "I'm sorry."

"Me too," he murmured.

Silence reigned on the balcony and for a moment she wondered if she should retreat inside to give him a moment even though they were in her quarters and they both had to get going; he had to talk to Jack to inform him of his decision before they dialed Midway Station. She was already reaching for her crutches when her 2IC spoke.

"You and General O'Neill," John started slowly, almost hesitantly. "I know it's probably none of my business but you're different around each other. Also whenever I went looking for him he was usually with you, or coming out of your quarters early in the morning. The ones assigned to him are pretty much unused and his bag wasn't even fully unpacked. At first I tried not to think anything of it but I saw you two yesterday on the pier when I needed him for something and you were talking and laughing… you didn't do anything inappropriate but it looked quite intimate, just by your body language. I'm not trying to accuse you of anything and what you do on your own time is entirely up to you but I just wanted to give you a heads-up because not everyone here might think the same way."

"Oh God," Sam muttered, covering her face with a hand. That was exactly why they had always refrained from touching each other or sitting too close for all the years they had worked together but now they had dropped the ball, thinking they weren't doing anything inappropriate but still betraying their feelings with the smallest gestures. "John-"

"Hey, it's really none of my business," he said quickly. "I mean, technically you answer to the IOA and even though General O'Neill is in command of Atlantis right now, you're on medical leave, so…"

God, this was embarrassing! "It's not like that… Well, it is but it's not what you think." She took a deep breath and tried to explain it. "Nothing ever happened while we were working at the SGC, I swear-"

"Whoa, relax! That never even crossed my mind, Colonel. I like to think I know you better than that."

"John, remember how I mentioned that stint at Area 51?" When he nodded slowly Sam let out a sigh before continuing with her explanation. "We weren't in the same chain of command at the time, so we, um-"

"Dated?"

Rolling her eyes, she groaned. That sounded so ridiculous at her age, it was almost as bad as when Jack had technically been her boyfriend. "Yes, so you can imagine that my 'temporary' reassignment to the SGC threw a wrench in our plans."

His eyes widened in understanding and he grimaced sympathetically. "Oh."

"Breaking it off wasn't an option, not after we'd waited for eight years… So, we got married instead."

"Right!" John exclaimed, grinning. "General O'Neill mentioned he had a wife!"

Sam frowned in confusion, wondering what else Jack had told her 2IC. "He did?"

"Slip of the tongue, I guess," he shrugged. "He was talking about how he'd rather be fishing with his wife at his cabin. Anyway, I'm glad to hear it. I'm happy for you; if anyone deserves it it's you two, probably."

"Thank you, John." She smiled gratefully. "We just prefer to keep it quiet because of our history but the higher-ups are aware of it and try to be as accommodating as possible in our line of work."

"Oh, of course! I won't tell a soul," he swore, still grinning. "Although it would be nice to just see the expression on Rodney's face…"

"Please, don't remind me," Sam said, grimacing. It had been hard enough not to blurt it out the day she'd arrived on Atlantis to take command and Rodney had come to her to talk about the 'unrequited lust' hanging between them. "Well, we should probably get going before Jack comes looking for us and tosses us both through the 'gate."

John laughed and handed her her crutches. "Yes, we wouldn't that."

He watched her with a funny expression as she took the crutches from him. "What?"

"Nothing," he said quickly. "I'm just happy for you… Sam."

"Thanks."

"It's nice to know that people in your positions can cope with such strong feelings for years and then overcome their working relationship after so long and still make it look so easy and natural…" His tone was almost wistful as his voice trailed off and he cast another glance at the sky. "It makes me wonder…"

Sam nodded wordlessly but doubted he saw it as he shook his head and walked away, clearly too preoccupied with his thoughts and she didn't want to intrude; they had already been more open with each other than she could have imagined. It was good to know John supported her marriage to Jack, even though her husband probably wouldn't be too ecstatic at learning her 2IC knew the truth about their relationship. Still, it was nice not to have to hide it from him anymore.


Gate Room, Atlantis
New Lantea, M35-117
Pegasus Galaxy

Jack waved off the people that had all gathered around to see him and Carter off and waited until they were all gone, or at least out of earshot before leaning in towards his wife. "So, ready for a twenty-four-hour quarantine at Midway?"

She beamed a smile at him and raised her brows suggestively. "Oh yes, I'm sure we can come up with something to pass the time."

"Why, I like the way you think, Carter."

"Thank you, Sir."

He rolled his eyes in mock exasperation, knowing she was only keeping up the pretense like the good officer she was. "Had I already mentioned I also managed to arrange for one of the ships in orbit to beam us over to the Pentagon from the SGC? That way we can take a car back to our place and enjoy the next few days together since I had my assistant clear my schedule for the rest of the week."

"Sounds good, Sir," she replied as the connection with Midway Station was established.

"Yep, just you, me and… well, nothing else, really."

Carter smiled wickedly up at him. "A bed would be nice."

"Right," Jack said, smirking. "I think that can be arranged. You need your rest after all, with that leg of yours…"

"Exactly! C'mon, let's go home."

Home.

Yeah, he couldn't wait to take her home and have her to himself for the next six weeks! "You betcha, Carter."

The End