Stargate Atlantis: S7 The Fossil Key

Part One: Prey Base

John Sheppard was brooding.

He sat alone in the conference room, which had become his impromptu office of sorts. He eschewed using the space that had once been the domain of first Elizabeth Weir, then Richard Woolsey. Instead his command post was the conference room and there he sat, a man alone and apart at a too large table surrounded by empty seats.

He reclined in the chair, long legs stretched across the table, crossed at the ankles. His combat boots and black pants were a dark stain on the wooden surface, harsh and dour. His arms were folded across the expanse of his lean, muscled torso, arms bare as the black t-shirt hugged his form.

He was a man in black, which matched his mood perfectly.

He licked his lips as his keen, emerald gaze was locked onto a single monitor, one among several in the room. He stared hard at the single screen, although not much was displayed upon it. It was a static-filled array of darkness and the planet on which Atlantis resided. It was a little blue ball spinning and spinning in the emptiness of space. Except that it wasn't quite empty.

Two indistinct blips hovered in orbit around the planet.

John scowled, shifting on the hard chair. He rubbed his chin, feeling the day's growth of scruff that lined his strong jaw but not caring. Shaving every day was the least of his concerns now. His gaze was locked onto that screen, onto those two seemingly inconsequential blips and what they represented.

The enemy was still out there.

It had been a month since Atlantis had been evacuated of all but a skeleton crew to keep watch. A month since John had made the command decision to sink the city and to keep it hidden from the new aliens that were threatening to destroy it. They were too powerful to meet head-on so John had no other option but to hide the city after evacuating nearly everyone from it.

He hated hiding but knew he had no choice.

Not since the Daedalus had been destroyed.

Not since the dialing to Earth had nearly drained a ZPM, leaving Atlantis woefully limited.

Still he would not abandon his post. He would maintain the expedition and defend the city to the death, if need be.

He hoped it would not come to that.

He had selected his skeleton crew very carefully, knowing that the fewer people the longer they would be able to hold out under the ocean and remain undetectable. Many had volunteered to stay, some even insisting, but John's decisions had already been made in his mind and his stance was quite firm on who should stay and who should leave. Some of the decisions had been easy; some hard, but all had been made efficiently without consulting anyone else.

The ones who had refused to stay still rankled, however.

One in particular still pissed him off, however much he had understood the reasons for her decision to abandon Atlantis.

He still felt a fission of betrayal at Teyla Emmagan's decision.

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"What?"

John's voice snaps like a whip, and he realizes he should have been more polite, but Teyla's words had felt like a punch to the gut and he had reacted almost violently.

Teyla is calm, as always, as she stands in her quarters. They are nearly empty as her belongings are already packed up and waiting with her husband Kanaan and their son Torren at the Stargate. "I have decided to return to New Athos, to help my people should these invaders to our galaxy head their way. I will not stay here in Atlantis with you, John."

John stares at her, uncomprehending for a moment. Emotions flit across his handsome face but he steels himself, revealing none of the confusion and anger within him. Or so he thinks as he stares at his friend and teammate. "Why? Do you think we will be destroyed after all?"

"No. If it was just me then of course I would remain with you here, in the city, even under the waves. But it is not just me anymore, John. I have to think of Kanaan and of Torren most of all. He will be safer on New Athos then here."

"I see. You think the fuglies will find us and destroy us? You doubt my ability to protect this—"

"Not at all. I will not risk my son, John. That is the point and nothing else."

"Is it? You really believe he will be safer on that planet? What if the fuglies show up? What then? What will you do? Offer them tea?" he sneers, unable to help himself. He feels betrayed although he knows that is not the case.

Teyla arches a brow at his remarks, but replies calmly, "I do. I must be with my people. Even though I am no longer their leader I am still of them, and I will do what is best for my son."

"I see."

"Do you?" she counters, dubious. "When you have a child you will understand. When Atlantis rises once more I shall be with my people and together we will greet you as allies and friends. Besides, would it not be prudent to have a trustworthy ally out there when you do raise the city?"

John grunts and nods briskly, conceding the point but he is still miffed and scowls. "If that's your decision, Teyla, I can't stop you. I don't understand it, but I respect your decision nonetheless."

Teyla smiles and steps to him. She touches his arm. "John, one day you will understand. I have no less faith in you to protect this city. When Atlantis is restored I shall return, have no doubt. But now I must put my son first, ahead of everyone, including you."

John sighs. "Things were a lot less complicated before you had that kid."

Teyla's smile broadens. "Indeed they were, colonel."

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John abruptly straightened in his chair, blinking to remove the two blips that even now danced in front of his eyes. He frowned, reaching for his bottle of beer. He sipped the amber liquid, finding the taste satisfying, distracting him from more serious concerns.

But not for long.

He glanced at the other screens. They intermittently flickered, relaying data through sporadic power cycles. Power must be conserved at all costs, and everyone has had that drilled into them repeatedly by Rodney McKay. Even with the central core of the city being the only part usurping power there is still a massive drain because of the shield holding back the ocean.

Rodney had set up a rotating power grid and so far the city was running smoothly under it. But as always the physicist worried about power consumption and every day he would ask John how long they would be imprisoned under the waves.

And every day John could only shrug and point to the two ships still hovering in orbit.

He wished he had an answer for his friend, for everyone, but he didn't. As long as the enemy lingered Atlantis had to remain hidden and silent, like a precious gem tucked away in the shadows and lost to all but a few who knew of her existence.

John smiled, thinking of his friend. He hadn't even had to ask Rodney to stay. The physicist had volunteered on the spot.

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"I've already calculated the needs of the city versus the power requirements of the shield and if we cut consumption down to only the core of Atlantis theoretically we could survive submerged for a few years, given the decrease in population and use of resources, of course, divided by the necessary primary systems to keep running online and the secondary defensive—"

John looks over as Rodney is walking next to him in the hallway, talking a mile a minute and continually referencing his data pad. "I didn't want to just assume you would—"

"Don't be stupid, John, of course I am staying so you don't even have to ask me because quite frankly you couldn't run the city without me, certainly not at such extreme power cuts despite your ATA gene and frankly I would be insulted if you even thought otherwise."

"Actually I was thinking of asking Zelenka to stay," John teases with a smirk as the two men round the corner.

The comment stops Rodney in his tracks and he looks up from his data pad. "What? Are you crazy? That is insane! Oh sure, Radek's a pretty good scientist but he is no way as competent in these more advanced systems as I am! What are you trying to do, John, sink the city and then just leave it there? You'll never be able to raise the city without me, let alone keep it running at on a substandard power grid while maintaining the shield at full power! And then there are the scans!"

"The scans?" John asks, as if having no clue.

"The scans!" Rodney flares, mistaking his friend's sarcasm for genuine puzzlement. "You will be wanting to run scans to see if anyone is out there! To see how long the fuglies will be in orbit or if the Wraith show up! And then there's the Penning trap! Only I can deduce its construction and somehow turn the thing into either an endless power source or a weapon!"

"I would prefer a weapon," John drawls.

"Of course you would," Rodney says with a sigh, but he sobers. "And after losing the Daedalus I think I agree with you. And trust me you don't want anyone else but me toying with a device that holds both matter and antimatter, no matter how small." He briefly smiles at his pun, but becomes serious. "I am staying, John, and that's non-negotiable."

John nods and briefly touches his friend's shoulder. "I wouldn't have it any other way, Rodney."

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John moved to his feet, gaze raking over the other screens. So far the scans hadn't revealed much except the fact that the enemy were still in orbit. There were two massive ships that had neither blasted the planet with weapons nor had attempted any kind of landing. The scans had to be sporadic so they would not be detected, but so far it appeared that the ruse was succeeding.

Atlantis was undetected.

For now.

John ran a hand through his hair, glancing at the monitoring of power levels, the ever-present consumption levels rising and falling before relaxing into a steady glut. He moved to another screen and tapped a key. Instantly the city responded and the tally of remaining Drones appeared.

The number was low, too low to even contemplate an attack. At least not yet.

Most of the Drones had been expended in the first assault, which had resulted in the serious damaging of a fugly ship, but it had been too many all at once and a careless waste of resources. John had not been to blame, however. It had been Carson Beckett who had relentlessly pursued that enemy ship, utilizing the second Ancient Chair that John had taken from a sister city and had joined to Atlantis' own Chair in a bold bid to bolster their defenses.

It had almost worked.

Until Carson had been too connected to the city and had begun to act erratically, using up nearly over half of the Drones. He had been injured as well, but Doctor Porter had saved his life and now the good doctor was fine and stable.

At least he appeared fine and stable.

John had begun to wonder about the doctor and his almost fanatical insistence to remain in the city.

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John strolls into the infirmary, weaving round clusters of medics and nurses who are busily tallying supplies. Many are teary-eyed as they prepare to depart Atlantis for Earth. He heads for a man in a white coat. "Carson? Will you stay?" He cuts to the point, having no time for any social niceties.

Carson turns to him, data pad in hand. He smiles. "Of course, John. I will stay."

"I mean there probably won't be any need for a doctor, but since you have the strongest ATA after me I just think we could use you when we…oh. You'll stay?"

Carson smiles. "Yes, John. I have no intention of leaving this city."

John feels a little unnerved by the doctor's smile and the brief coldness in his blue eyes. "Look, doc, I can't make you stay or anything. I'm just asking, and I wouldn't ask if I didn't think we had a chance of surviving this."

"I know that, John. Of course I am staying, so don't worry." The doctor turns away and moves to a group of medical personnel. "Like I'd leave her in your care?" he mutters with a trace of bitterness that is very unlike him.

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John walked through the city. Shadows chased after him, ahead of him as he passed beneath the emergency lighting. Small pools of amber lit his way, making the blues and the greens of Atlantis muted and hushed. Sometimes the lights briefly flickered as if greeting him and John acknowledged the city with a curt nod.

He made his way down to the armory. It was very dark, quiet, but John touched the wall and a soft light illumined the room for him. An array of weaponry greeted his gaze, rows and rows of P90s, Wraith stunners, a few bazookas and a case of C-4. Smaller guns were stored along one wall. Another wall was lined with lockers belonging to the various marines that had been serving under his command, had been serving Atlantis.

Most of them he had sent through the 'Gate back to Earth. The necessity of keeping the city's population dictated that he must sever himself from nearly all of the marines. If it came down to a fight in the city stealth would win out over sheer numbers. John was convinced of this. He had seen the fuglies firsthand and knew their strengths, both physically and through their weapons.

He had already lost a man to them.

Major Lorne.

John vowed he would not lose another.

Nevertheless he knew he would need reliable soldiers with him. He had selected two. Major Jason Reynolds had agreed to stay immediately. Ronon Dex had agreed as well, but John could see his friend's reluctance and he wondered at it. He realized it had nothing to do with ever doubting John's abilities or their chances of success, or even with his recent nuptials with Amelia Banks. It had everything to do with something else.

Ronon had been afraid.

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"What are our chances?"

As always Ronon cuts to the chase with a practical question, thus avoiding the verbiage that most people employ when answering a question. John smiles. "I'll take that as a yes, you'll stay?" The Satedan nods but there is a strange hunch to his shoulders that John has never seen before. "Fifty-fifty," he answers with a shrug. "Sixty-forty, maybe," he adds, seeing the skeptical look on his friend's face. "Look, I need a few men I can trust in a fight."

"You think it will come down to a fight?"

"It might."

"A face to face fight?"

There is a twitch to Ronon's face and John recalls how the Satedan had been seriously injured by one of the fuglies. He recalls hearing Ronon's scream and he hopes to God he never hears that sound again. "Probably not, but if it comes to that I need men I can trust in a fight. To defend this city at all costs. Men who have something worth saving besides the city." He hates playing that card but it is a necessary evil.

Ronon nods, considering. He shifts his stance as if the pain of his injury has returned. "You think you can win?"

"I think we can win," John changes the pronoun, stressing it. "So you will stay?"

There is a long pause, a pause pregnant with uncertainty. Once John would have been confident the Satedan would have followed him to hell and back, but not anymore. Something has changed and John doesn't know how to restore whatever Ronon has lost.

"Okay. I'll stay," Ronon says at last, but he looks far from happy about it.

"Thanks," John says, needing something to say. There's an awkward pause and then Ronon turns and leaves John standing in the armory, alone.

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John checked his 9mm then restored it to the holster on his thigh. Satisfied he left the room. He brushed his fingers along the wall and the lights faded to black at his command. His connection to the city was stronger now, as if after everything he endured for it somehow they are even more closely joined.

Except that the city felt different.

John couldn't explain it. He tried to blame it on the lower power levels, or on the fact that he only accessed the systems when absolutely necessary. It had nothing to do with the fact that the persona of the city had tried to literally absorb him into itself.

He still shivered at the memory of that cold, icy touch.

He knew that something was off, but he couldn't explain what it was. Everything was functionally normally and every system was in working order. Every simulation that Rodney ran came back fine. Still John knew something was off but he couldn't articulate it.

He had had even less success explaining to Richard Woolsey why he should stay with Atlantis instead of the expedition leader.

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"Because you can talk to the city? That's the reason you should stay instead of me?" Richard circles his desk, too upset to sit down. He circles it like a shark as John stands between the two chairs, undisturbed but surprised at the other man's almost vehement objections.

"Yes," John answers simply, but before Richard can begin his protest anew John continues. "And I am the military commander. It's my job to stay here and to protect this city at all costs by any means. Our people will need you at the SGC on Earth, much more than they will need me. It only makes sense that I remain here to guide the ship, so to speak."

Richard frowns. He is both angered and relieved at the same time and this makes him highly uncomfortable. "To follow your analogy, colonel, you will go down with the ship, as if you were the captain? I am the leader of this expedition and therefore it is my responsibility to—"

"To look after our people first and foremost. My job is to defend this city."

"And you can talk to it?"

John sours at the skepticism on Richard's face. "Yeah. Look, this ATA thing…it's stronger now. Much stronger than it ever has been so if we have any chance, any chance at all to save this city I have to be here with her, with it," he corrects quickly. He folds his arms across his chest as Richard stands at his desk, staring. "You take care of our people over there. I will take care of the city here."

"And if you can't hold out against the enemy?"

John shrugs again. "Then at least we will have saved as many as we can. At least we will have tried."

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John strode purposefully along the hallways, heading for the laboratories. Most were dark, silent, devoid of scientists, but a few were operational and utilized. It felt odd to be walking the halls of Atlantis. It felt like a ghost town where John was the hapless sheriff waiting for the bad guys to saunter out of the sunset and challenge him.

He smiled briefly at the comparison.

Water bubbled quietly in the walls, and as always he could sense and hear the quiet hum of the city's systems. He paused near a window to glance outside. Except instead of skyline and clouds the vast ocean depths met his eye. The cold blue water and killing pressure were held back by the city's shield. It was a pinkish veneer that turned the water's colors to a greenish violet murk. Fish swam by, darting this way and that, avoiding a collision with the giant spaceship parked in their midst.

It was like living in an enormous aquarium.

Hearing a woman's voice he quickened his stride. His boots clattered on the cold floor, sounding eerily loud in the mostly vacant city. A smile curved his lips, recognizing the voice and the tone, but his smile faded as more serious concerns filled his mind.

It sounded as if she was having yet another episode, another hallucination.

John found himself debating for the hundredth time if having Moira O'Meara remain behind with him had been a wise decision, or a harmful one.

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"The thing is…the thing is…the thing is I need you here. I mean I need your expertise on the fuglies, er, the Homo erectus," John quickly amends before Moira can correct him. He is uncharacteristically awkward but plunges onward. "And whatever's happening to you I think you would be better off here than there on Earth where they wouldn't understand what's going on, not like I do. And Carson will be here to help too. The thing is…the thing is." A gentle pressure halts his speech as Moira places her fingers along his lips.

Moira smiles at him, meeting his gaze at last, still uncomfortable over the changes to her one eye. The purple circle around her pupil is a result of the trauma she had experienced and she is shy about it still. "Of course I will stay, you silly man. You really think I would leave you? I, I mean I know you will need my expertise on the aliens and I am very close to deciphering their language plus I have a fuller DNA profile to—" she stammers as she is awkward now.

John smiles and gently moves her fingers from his mouth. "Thanks, Moy. You know that's not the only reason," he drawls, voice low as his arms encircle her and bring her closer to him.

Moira's hands slide up his chest, keeping a little distance between them. Only a little, however, as she is drawn to him like a moth to a flame and cannot resist. "I won't leave you, John. I…I can't."

"And I won't let you go, Moy." He leans close and kisses her, a soft brushing of his lips across hers with the promise of passion to come. "Besides…you still owe me an answer."

"What? I just gave you one, John! I will stay here with you and—"

"No, baby, not that." He smiles charmingly, freeing her and tilting his head. "I'm still waiting for a proper answer to my proposal."