CONNECTIONS

An epic story that starts in Atlantis after THE SEIGE episodes end and spans INTRUDER, putting the events of that episode into a lengthened, shippified, and detailed novalization of the events... I hope. I expanded the crossover with SG-1 to include everyone, so if you don't know who people are let me know and I'll put a synapsis in the next chapter for each character not normally seen on Atlantis.

This story is, at its heart, a romance between John and ELizabeth (Sheir, Sparky, whatever you choose to call it) with a tiny spattering of Sam/Daniel (SG-1 characters) on the side, but, nothing overly overt.

This story is rated M, but there are some parts that are rated higher that will not be posted on this site. If you want to read the story with EVERYTHING included, go to my site (link in my profile). I'll post a link later when I get the page online, as it's currently under constrcution.

DISCLAIMER: I OWN NOTHING. I DON'T EVEN OWN THE DVD'S FOR STARGATE: ATLANTIS YET. I DO, HOWEVER, OFTEN HAVE TO AVOID WALKING MY DOG, LINDEN, IN CERTAIN FOREST-Y AREAS BECAUSE OF FILMING FOR BOTH STARGATE SHOWS. A BIT ANNOYING, REALLY, THOUGH GETTING THAT CLOSE TO JOE FLANNIGAN AND MICHAEL SHANKS IS ALWAYS FUN. ANYWAY, FOR THE RECORD, I OWN NOTHING AND AM ONLY USING THE CHARACTERS IN THE FOLLOWING WORK OF FICTION AS AN HOMAGE TO THE BRILLIANCE OF THOSE WHO DO OWN THE STARGATE FRANCHISE. AND, OF COURSE, BECAUSE I LIKED TO PLAY WITH THE CHARACTERS THAT THEY HAVE SO BEAUTIFULLY CREATED AND WHO ARE BROUGHT TO LIFE BY AMAZING ACTORS. THIS CONCLUDES MY DISCLAIMER.

CHAPTER ONE

They had confirmed, as best they could, that the Wraith truly believed that Atlantis was gone, and Rodney and Zelenka had made sure that the cloaking device was still working. For the moment it seemed like Atlantis was safe from the Wraith.

The Daedalus had already started on its way back, the eighteen day journey having begun as soon as the ship was ready to make it all the way back to the Milky Way, and John and Elizabeth were busy assembling the files that they needed to bring back to Earth with them while Rodney and the other scientists worked feverishly to identify as many artefacts as possible before Rodney, Elizabeth, John, and Carson went back to Earth to report to the SGC and bring back increased staff in every department.

"I thought we sent all this stuff in that burst transmission a few weeks ago, the one with the letters and everything," John complained as he loaded a large shipping crate with files that he was sure Elizabeth had already sent to Earth in data stream form.

"Most of it was, but Colonel Carter sent a message with the troops. Apparently some of the data was somehow corrupted. All our personal messages were fine and were passed along after checking to make sure that no one let anything classified slip—Zelenka's was destroyed, and one of the Botanists' message had to be edited a little in the middle—but some of the actual files, especially mission reports, were incomplete or garbled in some way. Colonel Carter thinks it might have something to do with the compression program we used and the program that they used to open the files… I didn't quite follow, to be honest. Unfortunately, since she wasn't specific about which files were messed up, we've got to bring them all."

John cursed before getting to his feet, his back cracking loudly as he stretched his arms over his head. "That is not normal," Elizabeth frowned, cringing at the sound.

"A couple of hard landings and a pretty bad crash… I'm lucky this is all I have to deal with," John said.

"What did you fly?" Elizabeth asked.

"You've read my file," John replied.

Elizabeth smiled softly. "Not recently—your Earth file at least. I started new files for everyone here when we got here—that file I end up reading a lot, usually while you're recovering from something in the Infirmary," she said. "Plus I was never really all that good with the names of military machinery. I remember there being a lot of birds listed in your file, but my mind sees the name of a bird and a picture of an animal pops into my head."

"And that right there is where you and I differ," John said.

"I'm not disputing that," Elizabeth said. "So, what did you fly?"

John flopped down on the floor, his head resting on his jacket that he had discarded almost two hours earlier. "Everything they'd let me," he said. "Mostly helos; Osprey, Blackhawk, Apache, Cobra, those four were my main rides. But I'm qualified for F-14's, F-18's, most commercial planes, and, my personal favourite, my Stearman. It doesn't go as fast but it's the first plane I ever flew, and it's the only thing that my dad and I ever bonded over."

"Stearman… I don't think I know that model," Elizabeth confessed.

"I didn't figure you would. Open-cockpit bi-plane. I've got a fully restored one, the only thing my father was good for, he restored it and I got it when he died, but since I haven't been in the States for the past six years, except for my brief stay in Colorado before coming here, she probably needs some work," John said.

"Well, we're getting some time off, maybe you can visit… her," Elizabeth said, frowning at the 'her' even as she said it.

Rolling his eyes, John sighed. "It's perfectly normal for pilots to name their planes after the women in their life."

"I'm sure it is," Elizabeth said innocently. "So… what's your plane's name?"

"Samantha," John said with a smile.

"After… your girlfriend?"

"Nah. I decided a while back that girlfriends come and go, and it'd suck having to rename my plane every time I met someone new," John said.

"So… who is Samantha?"

John was about to respond when McKay came bursting into the office with a stack of files and a harried expression on his face. " Elizabeth, these won't fit with all the artefacts that we've been requested to bring back, can you find a place to squeeze them in with your files?" the astrophysicist said, out of breath and covered in rivulets of rather dirty sweat.

"Uh… John? How much room is left in that crate?" Elizabeth asked.

"Put them on the chair. I'll make sure they get in… somehow," John promised. He looked over at Elizabeth. "We've been doing this for five hours. I haven't eaten for two days and that was a wilted salad-like-thing that I still don't think is food on the grounds that it was vibrant neon pink with orange stripes, though Teyla says it's got almost everything that Beckett told her we need in our diets. I've reached a point where your laptop is literally turning into a giant cartoon steak with butter-smothered green beans and a scoop of mashed potatoes."

"I hardly think your situation has become that dire, but you are right, we have been at this for a while," Elizabeth said, her eyes flicking to her watch, though it was probably not accurate given that it was unlikely that the planet they were on had a twenty-four hour day—none of the scientists had been able to accurately determine how long one day was, though, to be fair, they had had their hands full with other more important matters since arriving in their new home. "How much more time do you need, Rodney?" she asked.

Rodney thought about it for a moment before answering. "A few hours, a day at most. Zelenka has some calculations pending that should be included, and there's a device from M7Y-396 that still has to complete the final quarantine stages before it can go anywhere. Other than that my department is good to go," McKay said.

"And you've got the suggested personnel lists for sub-sectors that you're not actively involved in?" Elizabeth asked.

"Still waiting for xenobiology to give me their list, but it's a pretty small pool to pick from so if need be I can just go over the files that the SGC has on hand," Rodney said. "Anyone in that field that they could request is probably stationed either at Area 51 or the SGC itself."

"Good," Elizabeth said. "Now, and I mean this in the kindest way possible, please go take a shower before someone tosses you off the balcony into the ocean."

Rodney frowned. "Excuse me?"

"She's saying you stink, McKay, and I have to agree with her," John said bluntly. Rodney looked over at Elizabeth who made a face that told him that she really hadn't wanted to say anything but that she agreed with Sheppard, and, with an offended cry, Rodney threw his arms up in the air and turned around, stalking away, heading for the nearest shower Elizabeth hoped.

After making sure Rodney's artefacts were in the crate, John looked over at Elizabeth. "So… day after tomorrow we head for home." He frowned, not liking the way that sounded, though he couldn't put his finger on why.

"Day after tomorrow sounds good," Elizabeth agreed. "But we're not going home," she corrected.

Immediately understanding what she meant, John nodded, smiling softly. "You're right. This is home now," he said softly. He stood up and dusted off his pants quickly. "Lunch?" he said, motioning toward the door.

"I promise not to force anything pink and orange on you," Elizabeth smiled.

"Ugg, don't remind me," Sheppard said, shuddering dramatically as he placed a gentle hand on the small of Elizabeth's back, unconsciously leading her out of her office and toward the corridor that would lead them to the Mess. "I don't care that this is another galaxy. Nothing that looks like that stuff should be allowed to be called food."

The rest of that day was spent finishing up mission reports and gathering letters and messages for people back home—they had all sent their videos a few weeks earlier, but the general tone of those messages had been fatalistic at best and the majority of the staff wanted to give their loved ones a more upbeat message now that they were out of the immediate woods regarding the Wraith.

John and Elizabeth had little else to do once they had packed up the files and gathered the messages, so they spent their last day on Atlantis before returning to Earth wandering around the city and bothering people who had more than enough work to do.

Carson spent the day going over patient care instructions with Doctor Biro and those with medical qualifications, the wounded from the Wraith attack on Atlantis still convalescing in the Infirmary, some in need of constant monitoring; he had tried valiantly to use that as a reason to stay on Atlantis, if only so that he wouldn't have to go through the Stargate more than absolutely necessary, but Elizabeth had been firm in her decision that all of the Senior Staff return to Earth.

And Rodney spent the day working, unwilling to admit that a great many of the scientists on his staff could, would, and had done most if not all of the tasks that he undertook, determined that he was the only one who could make sure that Atlantis remained safe until his return which, if things went according to schedule, wouldn't be for at least a month, probably longer.

Late that night the four Senior Staffers all found themselves raiding the kitchen, unable to sleep in anticipation of what they were going to do the next morning.

Elizabeth, wearing a tank top and a pair of well-worn sweatpants with the word GEORGETOWN printed in cracked lettering down the left leg, remnants of her tenure as a professor, was the first to arrive. Her goal was a cup of tea, the good stuff from back home, not the Athosian tea that Teyla still drank every morning to prepare herself for the day. She was tapping her toes on the floor, making her bunny slippers dance, while waiting for the camomile tea to saturate the hot water she'd poured over it, when she heard someone clattering through the Mess Hall, heading to the kitchen.

Not surprisingly Rodney stumbled in next, a coffee cup clutched in his left hand, still dressed in his uniform, his lab coat that he so rarely wore showing signs that it had been set on fire very recently, possibly only minutes earlier judging by the faintly smoky smell that Elizabeth caught as the exhausted astrophysicist brushed past her in his single-minded pursuit of his beloved caffeine.

John arrived shortly after Rodney, barefoot, a pair of track pants resting low on his hips, a sweatshirt half-zipped up over his bare chest. His plan had been to hit the gym to try to work off some of the excess energy he seemed to have, but he had been halfway to the gym when he realized he wasn't wearing shoes and so he had changed directions, thinking that maybe a snack would help him. If not sleep, then at least focus so that he didn't forget to wear shoes again—the Ancients had been pretty advanced, but they hadn't thought to install heated flooring when they built Atlantis.

Carson was the last to arrive, having come straight from the Infirmary to the mess hall after his shift ended, his evening meal having been scheduled around midnight for the past few months, and the Scot was more than a little surprised to find that the kitchen was rather full when he showed up for his dinner. Though, he did have to admit, he was even more thrown by the attire of his friends—Rodney and his charred clothing wasn't too out of the ordinary, though the fact that the left pocket was still smoking a little was; Sheppard with no shoes was strange, the Major usually being ready for anything, and, in Carson's opinion, that usually meant that shoes were a good thing to put on before leaving your room; and Elizabeth, looking more like a college co-ed than the leader of a scientific and military expedition to another galaxy dressed in her Georgetown Hoyas' sweatpants and matching tank top, not to mention her bunny slippers and bed-tousled ponytail.

"Mass insomnia. Notta good sign," Carson said, trying for cheerful but missing the mark.

"I've drank two full pots of coffee since dinner. I couldn't sleep now if I wanted to," Rodney said, talking faster than normal, something John hadn't thought was possible. "But if I don't continue drinking coffee I'm going to completely crash somewhere around six in the morning, and after I come down off a caffeine high I can sleep for days if I'm not careful."

"I'm just feeling restless, Doc," John assured Carson. "Haven't been off-world in a while; I'm feeling kinda stir crazy. It got worse when someone," he said pointedly, his eyes directed at Elizabeth, "gave me the time to departure right down to the second."

Elizabeth cringed. "Sorry. I do that when I know something big is happening," she said. "Eight hours, twenty-one minutes, forty-seven seconds," she added after glancing quickly at the clock on the wall. John let out a loud groan of frustration and Elizabeth cringed again. "Sorry, John. It's… it's something that's out of my control. I've done it since I was a kid. When my best friend was counting how many sleeps there were until Christmas, I was counting hours, minutes, and seconds, until Christmas morning.

"Why?" Rodney asked.

"We had a ritual at my house. Six o'clock wake up call—that was when my mental clock hit zero. After that it was officially Christmas. Mom and dad going into the kitchen to start breakfast while my brother and I went straight to the tree to see how much the pile had grown overnight. Big pancake breakfast, then we'd all do the dishes together—a very messy operations—and then we'd put the dog outside—he always wanted to help open presents which had been fine until the suede handbag my brother and I saved up to buy my mom was destroyed by doggy drool—and we'd go in the living room and light a fire and open all of our presents in a mad rush because the annoying and typical presents were on the outside—socks, sweaters from Great Aunt Gertrude, stuff that no one asks for and unimaginative relatives buy in bulk to make sure that they have gifts for everyone in the family—and the good gifts, the ones that we'd actually asked for, were buried in deep, but dad had a rule, and there was only one rule, and that was that we work through the presents in layers from the front to the back," Elizabeth said. She shrugged. "I kinda feel like that right now. Like when my mental clock hits zero it'll be Christmas morning."

"Except it won't 'cause when we get to Earth there will be a full and thorough, and probably invasive, physical, followed by several days if not weeks of intense debriefings, followed by your horrible trip to Washington to do the politicking thing," John said.

Elizabeth rolled her eyes. "First of all, if it weren't for a lot of these people the Stargate program would have been shut down well before Doctor Jackson figured out that it took eight glyphs to dial Pegasus, so, as much as I may not like the way I'll have to be while I'm there, I'm prepared to… do the politicking thing," Elizabeth said, "for the sake of both programs. And second, I'm being forced to Washington for a week or more, and while I'm gone you three get to go on vacation. Carson's already got tickets waiting for him to take him to Scotland to see his mother."

"I do?" Carson frowned as he gathered together the leftovers from dinner to make himself an evening meal.

"You're the only one of the three of us who has family to visit, Carson. The SGC was glad to foot the bill for a return-trip ticket for you to see your mom," Elizabeth smiled. "And you two," she said, turning to John and Rodney, "are going to have full access to anything you want within Cheyenne Mountain. One of their science labs has been emptied out for you, Rodney, and John, there are at least four SG teams that I know of that have offered to take you on as a fourth or fifth if you were interested in going off-world in a different galaxy."

"Cool," John smiled. He had been worried that he would be stuck on base doing absolutely nothing except recruiting new military officers to the Atlantis mission. Well, actually, he was most worried that he would be pulled off the expedition, or that they would send a new military commander to take his place, someone with a higher rank and political friends who could pull the right strings, but he was also worried about being stuck in the SGC with nothing to do.

"Well, I have to say I am certainly looking forward to working closely with Lieutenant Colonel Carter while we are back on Earth," Rodney said, the lascivious tone in his voice making his friends cringe.

Elizabeth shook her head. "Rodney, the woman can not stand to be around you," she said.

"Our relationship is a complex one, I admit, but I hardly think she can't stand me," Rodney said.

"Lieutenant Colonel Carter? Which one is she?" Carson asked.

"SG-1," Elizabeth said.

Carson nodded. "Yea, Rodney, Elizabeth's right. She 'canna stand ya."

Firmly in denial, Rodney shook his head. "She is simply reluctant to allow her true feelings come forth. Emotion in the military is frowned upon, you know, and it's hard for women, especially beautiful blondes," he said, his usual condescending self heightened by the lack of sleep he'd been surviving on for weeks.

"Okay, first of all, cut the sexist crap, Rodney, or you'll join Kavanaugh on the deserted planet I've been promising him," Elizabeth said, "and second, I know that she can't stand you because she told me that she can't stand you. Something about wanting to force a lemon down your throat whenever you open your mouth."

"Ouch," John said with a small smile. He had threatened the scientist with citrus more than once since they met; there was hardly anyone who hadn't, John was sure. "I think I'm gonna like this Colonel Carter," he said.

Elizabeth tensed slightly, but not enough that anyone noticed. "I'm sure you will," she said before throwing out her teabag and making sure she hadn't left any mess behind. "I'm going to try to get some sleep," she said, taking her tea with her as she walked out of the kitchen, though the mess, and into the halls of Atlantis.

TBC...

Like it? Hate it? I swear, it gets better once they get to Earth.

Let me know what you think.

Manic Penguin