Extract from Stargate Atlantis The Chosen ©MGM and Fandemonium. All rights reserved.

Prologue

Somehow he felt just a little cheated.

Sitting on the grass, the mid-afternoon sun warming his face and the breeze ruffling his hair, Major John Sheppard decided that this day was just about perfect in every way. The brilliant blue sky—ideal flying weather, the aviator in him noted idly—was completely inappropriate for the magnitude of the decision he was about to make. Storm clouds would have been more fitting, or at least something with a little less cheer and a little more drama. Figures. He allowed a wry grin to twist his lips. Unpredictability seemed to define his life.

Taking the road less traveled was one thing, but he was pretty sure Robert Frost had never considered that it might lead to another galaxy.

God, another galaxy. He still hadn’t wrapped his mind around that concept. Days ago, he’d been minding his own business at McMurdo Station, secure in his view of the world: namely, that it was far from perfect but at least followed a rational set of rules. It was quiet, he was getting lots of stick time, and the environment, while hostile, didn’t come with gun-toting inhabitants determined to blow him out of the sky. At least, that’s what he’d thought until that freaky missile had fired at him. Then he’d taken a seat in that equally freaky chair, and everything that he’d thought he understood about the world had gone out the window.

It was an unparalleled opportunity, they’d all told him with the same expression of wide-eyed wonder. Travel instantly to another galaxy, explore the culture and technology of a race far more advanced than our own, and take a stab at defending Earth from a nasty fate. He was a strong natural carrier of the all-important gene. Think what they could do with his help. There was just that one tiny detail about possibly never coming home.

It surprised him that he wasn’t more afraid of that prospect. Then again, he wouldn’t exactly be leaving behind a stellar career and devoted family, and Antarctica was already about as close to an alien environment as he could imagine.

Still, another galaxy?

Leaning back against the hillside, John wondered if the idyllic weather was a sign. He dismissed the thought when he couldn’t be certain if it was telling him to stay on Earth, where there were lovely sunny days, or to consider this ‘opportunity’ a step toward a brighter future. And because he couldn’t interpret the potential omen and had no better luck interpreting his own turbulent thoughts, he returned to his original plan.

Years of special-operations flying had instilled in John a deep respect for mission planning. He’d chosen the site and the time of day, selected the unit coin, even checked the wind direction; though that might have just been his inner aviator again, hoping irrationally to get in one last flight before reporting to Cheyenne Mountain. He had planned out every last detail of this life-altering decision—then placed his future squarely in the hands of fate.

Tails meant returning to the status quo at McMurdo, where they got the football games on videotape a week late but at least no one asked him about Afghanistan. Heads meant a potential one-way trip through a big metal ring that would dump him out…somewhere else.

He stared hard at the coin, then flipped it into the air. It spun gracefully, the sunlight glinting off its face, and landed with a satisfying smack against his palm.

Tails.

Apparently fate was telling him to stick to his own galaxy.

And yet—what if they really didn’t have anyone else with the same knack for operating that weird equipment? What if they somehow needed a pilot? What if, through some thoroughly unnatural confluence of events, that other world ended up giving him the sense of purpose he’d misplaced somewhere along the way?

No. He’d left the decision to fate, and fate had slapped him with tails. End of story.

And yet…

John Sheppard had never been particularly good at blind obedience. He shot the coin a look of contempt, then flipped it again—

Chapter 1

"Heads!” Aiden Ford announced, his boyish features alight with triumph. “Victory is mine.”

Teyla’s brow creased. “What have you won, Lieutenant?”

“The last brownie.” Pocketing the coin, Ford grabbed the desired treat and plunked it onto his tray. Stackhouse walked away with slumped shoulders.

“We still have brownies?” John Sheppard’s eyebrows shot up as he settled into a seat at the nearest table.

“That was the last one.”

“Damn.”

“Yeah.”

“Please tell me the defenders of our fine city aren’t spending their time mourning the lack of desserts.” Rodney McKay announced his arrival with a characteristic scoff.

After the waking nightmare that had been the storm and the concurrent Genii assault on Atlantis, they’d all gained a new sense of ownership, for lack of a better term, in this place. It was their home, damn it. They’d paid for it in every way imaginable. Right now, just being able to sit here and argue about dessert was enough to provoke a sensation of deep relief in John Sheppard. It was normal, and normalcy had been in short supply from day one.

“You’re getting on our cases about provisions?” Ford looked indignantly across the table at Rodney. “After your little one-man melodrama with the coffee?”

“Do I need to explain the debilitating neurological effects of caffeine withdrawal again?” the scientist fired back.

“No,” John cut in, glancing over at their Athosian teammate. “Teyla? A little mystified by this overdose of Earthly idiosyncrasy?”

Teyla looked grateful that someone had brought her back into the conversation. “I am still pondering this ‘coin toss’ Lieutenant Ford spoke of. It is a contest of some kind?”

Ford withdrew a coin from his pocket. “We generally use them as currency, but sometimes we use them to make a choice by tossing it in the air, and assigning a decision to whichever side lands face up.”

“Would it not be more beneficial to weigh the positive and negative aspects of each option, rather than make a choice at random?”

“Well, yeah, but there are times when both options seem equally right, so you leave it to chance, fate.”

“I see.” Her tone suggested that she didn’t. With long fingers, she plucked the medallion from the Lieutenant’s hand and studied it. “The design is intricate.”

“That’s the symbol of my Marine division.” Ford pointed to the crest. “There’s a tradition that says if someone catches you without your unit coin on you, you have to buy them a drink.”

“A drink?” Teyla cast a curious glance at him.

“Of alcohol, preferably,” John elaborated, reaching for his glass of water. “But if there are any stills cropping up around here, Lieutenant, I don’t want to know, because I’d have to put the responsible parties in my weekly report. And you know I like to keep those as short as humanly possible.”

Ford’s expression froze somewhere between a knowing grin and feigned innocence. A second or two passed before he opted for a change of subject. “You got a challenge coin, Major?”

“What? You thought it was just a Marine tradition?” John reached into his back pocket, withdrew a scratched silver coin, and handed it to his second in command.

“Special Ops. Cool,” said Ford, reading the designator. “Bet you’ve got some hardcore stories to tell, huh, sir?”

On second thought, maybe that hadn’t been such a bright idea. “Stories, yes—stories to tell, not so much.”

“Because you can’t say? Or because you don’t want to?” The young man’s expression betrayed his naïveté.

“Little of column A, little of column B.” For John, part of the allure of the Pegasus Galaxy had been the fact that, here, his record wasn’t nearly as remarkable—and not in a good way, either—as it was on Earth. He’d been happy to let the Marines believe that he was nothing more than a throttle-jockey, rank notwithstanding. His days of relative anonymity on that front were probably over, thanks to his star turn during the Genii attack. Now, there could be no denying his… What was the proper euphemism? Breadth of experience? The trail of dead Genii in his wake during the storm had seen to that.

Then there’d been the unrelenting thud of bodies striking the ‘gate shield, one after another, until a rational person could no longer keep count.

Deliberately shoving that thought aside, John grabbed something that passed for a French fry off Rodney’s tray before redirecting the conversation. “I used that to decide whether to come along on this little road trip.”

“To Atlantis? You flipped a coin?”

John shrugged, choosing not to complicate the issue with details. Rodney, of all people, nodded understanding and pulled something from inside his jacket. “I keep a Loonie around for just such contingencies.” He held it out to Teyla, pointing to the bird on the dollar’s face. “This is legal currency in my home country, as opposed to whatever those two are carrying around.”

Behind a tall glass of Athosian fruit juice, Ford was hiding a smirk.

The Canadian scientist made a great show of turning to him in mock curiosity. “I presume you have some brilliant play on words to share? Because, gosh, I’ve never heard a Loonie joke before.”

“No, nothing.” Ford made a valiant attempt to resist the urge to make a wisecrack, but ultimately failed. “It’s just… Is that a Loonie in your pocket, or are you just happy—?”

John groaned and lightly smacked the back of the Marine’s head. “A wide-open shot like that, and that’s the best you can do? Not only are you banned from naming things, you’re relieved of mocking duty.”

“Yes, hilarious, Lieutenant. Did I miss your thirteenth birthday last week?” Rodney glared across the table at them both, but then his attention was diverted by a minor commotion. A huddle of three engineers, expressions running the gamut from irritatingly determined to determinedly irritated, strode into the mess hall.

“This oughta be good,” John muttered to Ford.

As the trio neared the team’s table, their back-and-forth chatter became audible. “I’m telling you, it wasn’t the power surge. It was—”

“Yes, yes, we know. Something else. Helpful suggestion, that.”

“Dr McKay,” the female member of the gang began. “We’ve run into a problem with the life-support systems.”

Regarding the three-person squad with mild interest, Rodney seized the last of his fries before John could sneak any more off the plate. “A little clarification goes a long way, people.”

“The storm caused a lot of damage.”

The remark had fallen casually from the engineer’s lips. Damage. That was one way to put it. John cast a surreptitious glance at Rodney.

While the scientist’s face didn’t overtly change, he tugged unconsciously at the sleeve over his bandaged arm, legacy of a Genii-style interrogation. “As usual, I’m impressed by the collective talent this group has for understatement,” he grumbled.

That sounded enough like Rodney’s normal self for John’s concern to fade somewhat. Normal was good. Hell, even fake normalcy was worth something, because eventually they’d start to believe it.

“Right,” replied the engineer. “Well, with the city’s help we were able to restore primary life-support power shortly after the storm. Problem is, there are facets of the system that the city doesn’t consider crucial. Potable water is critical, for instance, but waste disposal apparently isn’t. Hence, a few days’ worth of waste, even with a group as small as ours, is beginning to strain the capacity of the storage tanks.”

Of all the things that could cause problems on an intergalactic expedition, the possibility of clogged toilets had never entered John’s mind. Eat your heart out, Buck Rogers.

“And this relates to me in what way?” Rodney wanted to know.

“Kwesi thinks that—”

“Kwesi thinks that he can speak for himself, thank you,” another of the engineers cut in, his gentle Ghanaian accent sharpened by annoyance. “It takes someone with the ATA gene to make much of this technology work, Doctor. We believe that if you could interface with the city systems, you might convince it to rearrange its priorities.”

Rodney still looked nonplussed, but John imagined that he could see a glint of something new there. Pride, maybe. Rodney had successfully received the gene therapy, and there was something to be said for being one of the select few to have the magic touch.

“As flattered as I am that you see my potential for a job in sanitation, the city seems to like the Major here better than me.”

John’s focus snapped fully into the conversation. He got the distinct impression that he’d just been volunteered for something. “Say what?”

“Well put, as always,” Rodney muttered dryly.

“But you know the systems better than anyone, Doctor,” countered the female engineer, whose name John still hadn’t learned but whose skills at buttering up the boss apparently were top-notch.

“I suppose duty calls, then. I should have had overtime pay built into my contract.” Rodney rose from the table. Mess hall tray clutched in his hands, he somehow managed to adopt an air of unwavering self-assurance. “Lead on.”

The rest of the team followed, picking up their trays and carrying them to the cleanup area. Ford reached down to save his hard-won brownie and discovered it missing. He jerked his head up just in time to see Rodney pop the last bite into his mouth.

“Hey!”

“Don’t disparage a man’s national symbols or his coffee habits, Lieutenant.” The astrophysicist’s voice was entirely unapologetic.

John tried not to crack a grin at Ford’s crestfallen look. This version of ‘normal’ felt a little forced. Still, it was a start.

*

The computer screen stared at her, blank faced and accusing, until Dr Elizabeth Weir gave in and leaned back in her desk chair, massaging her temples. The gritty sensation behind her eyes warned her that she might be coming down with something. She told herself that it was probably just stress brought on by recent events. Nevertheless, she made a mental note to have one of the engineering teams analyze the city’s biohazard containment capabilities. While they’d brought HAZMAT gear with them, it would be good to know what facilities the Ancients might have installed in the city. One never knew what new pathogens lurked in this galaxy.

That small seed of data fell into a jumbled pile with all the others she’d collected over the past months. Precious few were finding an appropriate place to take root. There was so much to be done, so much to be learned. It was far more than they could possibly grasp in a lifetime—even if they weren’t stumbling into adversaries every other day. What had begun as an expedition to the lost city of Atlantis had almost immediately turned into a continuous battle for survival; against man, beast and nature, often simultaneously.

Had she honestly expected any less? When SG-1 had first stepped through the Stargate years earlier, they had opened the proverbial Pandora’s Box. That Atlantis was presenting similarly daunting challenges should have come as no surprise.

During her brief tenure as head of Stargate Command back on Earth, Elizabeth had learned that some enemies were, as Daniel Jackson had pointed out, pure evil. The Wraith might or might not be evil, but they assuredly were vicious predators to whom humans were nothing more than food. How was a person bred for diplomacy meant to face an opponent with whom there could be no negotiation?

A knock on her door interrupted her thoughts. Probably just as well, despite the fact that she hadn’t yet managed to write word one of her report on the events of the past week. “Yes?” She looked up, an expectant smile firmly, if artificially, tacked in place, to see the tousled dark hair of Major John Sheppard.

“Hey.” His smile was cautious, not quite reaching his eyes. “You busy?”

“No! No. Come in, John.” She stood and walked around to the front of the desk. “Actually, you’re just who I wanted to see. It occurred to me that I never thanked you for taking down Kolya. I’ve never had my life saved quite so…directly before.”

The Major seemed to shrug off her gratitude. “Had to make sure I didn’t get stuck with all your paperwork.” He eased into the room and the glass door slid shut behind him. “How’re you doing?”

His gaze remained guarded, betraying the weight of the obviously loaded question. Elizabeth didn’t take offense at his concern. During her years negotiating peace agreements, she had encountered more than her fair share of moral lepers, people who regarded the lives of others with no more compassion than she gave to the contents of a trashcan. She’d seen that same look in Kolya’s eyes, heard that same tone in his voice when he’d held her and Rodney captive. Before, though, she had always seen such things from a distance. With Kolya, she’d been close enough to feel the coldness.

Gesturing for the Major to take a seat, she leaned back against the desk. “I just wish it could have gone another way.”

“Listen—”

“I know!” She held up her hand. “I know that the Genii attacked us first. I know they’ve been deceptive from the start. It’s just that they’re not Wraith. They’re human, and the Wraith are far greater enemies—to both of us. It’s such a waste for us to be fighting one another.”

“Is that how you think it works?” John asked with a humorless chuckle. “In your experience, have people ever been all that great at setting aside their differences and working together in the face of a common foe?”

Taken aback by his uncharacteristically acerbic tone, Elizabeth examined John more carefully. She’d wanted him on this expedition because he carried the Ancient Technology Activation gene, and more significantly, used it without any apparent effort. Just as importantly, he’d enjoyed working with the highly individualistic people in the confined and hostile environment of McMurdo Station. Military background notwithstanding, Major John Sheppard had proven to be a surprisingly good diplomat; perhaps better than any of them, herself included. If anything, he’d seemed almost too trusting, too friendly—until they’d encountered the Genii.

The surgical precision with which he’d systematically taken out each of the attacking Genii, the way he’d aimed at Kolya and fired without a second thought… She could still feel the hot whine of the bullet as it sped past her ear. Her very next memory was of him offering her a hand and asking her if she was okay. With sudden insight, Elizabeth realized that, despite his professionalism, what set John Sheppard apart from men like Kolya was the way he reacted to killing.

Wondering if he himself could see that distinction, she said, “I’m trying to tell myself that we can’t hold ourselves responsible for the Genii’s actions. It was their choice to see us as an enemy. Likewise, if you’re still rethinking your decision to close the shield, please don’t. Yes, a lot of their soldiers died, but you and I both know what they were coming here to do.”

He cast a sharp glance in her direction, but a knock at the door cut the metaphorical thread. Peter Grodin was looking through the glass panel. She considered asking him to wait, but his excitement was obvious. Opening the door, Elizabeth stood back for him to enter. “Yes, Peter?”

“Dr Weir!” he declared. “I think I’ve found one.” Peter’s eyes darted to Sheppard. “Sorry, Major. Am I interrupting?”

“One what?” said John, standing.

Feeling a surge of anticipation, Elizabeth replied, “I asked Peter to work backward through the database, to locate the worlds most recently visited by the Ancients before the city was placed under siege.”

“Before they accepted the possibility that the Wraith might defeat them?” John’s interest was obviously tweaked.

“Of course they could still have visited those worlds via the Stargate, even after Atlantis had been submerged,” Peter explained as they left the office and crossed the walkway to the control room. “We assumed that, by then, they would have been concentrating their resources on defending Atlantis. If the Ancients were forced to abandon outlying worlds in a hurry, they might have left a ZPM behind, one that’s only ten to fifteen thousand years old. Which is exactly what appears to have happened with P3Y-986. Here, come and have a look.”

Peter moved in front of the large flat-screen monitor mounted on a panel behind the DHD, and tapped the screen. “The Ancient database indicates that the Stargate is in orbit around the planet.”

“We still don’t know why they placed certain ‘gates in orbit,” said Elizabeth.

“Quarantine?” The Major’s brow creased, and he rubbed the side of his neck where the iratus bug had been attached. “Having a ‘gate in orbit would’ve restricted travel to space ships.”

“That’s a reasonable assumption.” Elizabeth nodded. “We can send a MALP through. That would tell us for certain.”

“Why don’t I just take a puddle jumper? We can’t afford to keep losing MALPs.”

“I agree with that,” Elizabeth said, looking at him. “But we can less afford to lose you if there’s a Wraith ship—or worse—waiting on the other side.”

“Fair enough,” he said slowly, his smile suggesting a compromise. “How about we get the puddle jumper ready, then send a MALP through ahead of it? If it looks okay, we go, recover the MALP and—”

“How can anyone be so stupid?” demanded a loud, familiar voice.

Elizabeth’s enthusiasm was tempered by resigned amusement—which quickly turned to distaste. Leading a delegation of three extremely angry people in her direction was Dr Rodney McKay. At least, it was someone who walked and sounded like him, but it was hard to be certain because he was—

“Having a crappy day, Rodney?” John quipped, keeping his distance but looking remarkably cheerful.

The sight and smell of raw sewage wasn’t new to Elizabeth; she’d spent plenty of time in dirt-poor villagers in third world countries. But seeing Rodney literally covered in effluent, stomping across the pristine floor of the control room, was so bizarre that she had to stop herself from laughing.

“Oh, yes, biohazards are a laugh riot, aren’t they?” When it came to sarcasm, Rodney existed on a wholly separate level from anyone else she’d ever known.

“Well, it was your suggestion to try it!” declared one of the equally filthy people accompanying him.

“You could have at least warned me!”

The argument gained volume. From what Elizabeth could make out, it sounded like some sort of explosion was involved, but beyond that, the details seemed to be in the eye of the beholder. “All right, everyone. Calm down,” she called. “Now, is anyone hurt?”

“Calm down!” Rodney spluttered. “Calm down? It’s not enough that I’m probably going to catch pneumonia because some lunatic forced me to work outside in the middle of a hurricane. Do you have any idea of the number of pathogens that inhabit a septic tank? If just one of the billions, billons, of bacteria gets inside this cut—” He pointed to his arm. “Rampant septicemia. That’s it,” he added conclusively. “I’m gone!”

“Why don’t you go get cleaned up and have Carson check you over before we discuss what happened?” Elizabeth suggested.

Rodney’s expression managed to turn haughty, quite a feat considering the brown sludge on his face. “Because I wanted you to see with your own eyes—”

“Okay, Rodney,” she replied in a well-practiced pacifying tone. “I can see.”

“And smell,” John added, ever helpful.

Behind them, half a dozen people snickered. Elizabeth did her level best to ignore them. “Now, was anyone else…injured in this explosion?”

“No, but that’s beside the point. This is just one more example of—”

“Ah!” Elizabeth wrinkled her nose and motioned in the direction of the living quarters.

The arguing group, still led by Rodney, made its way out of the control room, although the noisome smell lingered.

“Well, that ought to make him the butt of a few more jokes,” John said.

The sniggers in the control room were louder. Elizabeth shot him a reproachful look. “Try not to aggravate him too much, Major. He’s been through a lot lately. We all have.”

Sheppard's expression conceded the point. Turning his attention back to the screen, he gestured toward the symbols on the display. “So, you want us to go take a look?”

“Why don’t you wait until tomorrow morning? That’ll give Rodney time to get cleaned up and calmed down.” At the Major’s look of uncertainty, she added, “Do you have a problem with that?”

“No. McKay can be a pain in the ass—and no, I didn’t mean that as a joke—but he’s got his uses.”

Unless she was mistaken, John Sheppard was beginning to like the scientist. “All right. In the meantime, I’ll go talk to Rodney, find out what happened.”