Stargate Atlantis: Sleep Before I Do

By: Shadow Chaser

Title: Sleep Before I Do

Author: Shadow Chaser

Disclaimer: Stargate SG-1 & Stargate Atlantis and its characters are the property of Stargate (II) Productions, Showtime/Viacom, MGM/UA, Double Secret Productions, Gekko Productions, AcmeShark Productions, and Scifi Channel. This story is for amusement only and I didn't get any money for it. No copyright infringement is intended.

Summary: On a mission to M3R-154, the team is ambushed by aliens working with Kolya's rogue Genii. Taken to their underground lair, they discover something shocking and sinister. A race long forgotten will be awakened and the discovery of a weapon may just turn the tide of the war – if the team survives.

Rating: PG-13/R

Status: Part of a trilogy (1/3); Complete

Content Warnings: Lots of character whumping, H/C, battles, violence, torture, etc. Whenever Kolya's involved, you know there's gonna be people hurtin'. ^_^

Spoilers: Up to Phantoms (everything after that makes this story AU)

Category: Action Adventure, Drama, H/C

Pairing: Hints of Shep/Weir, Shep/McKay friendship, hints of Ronon/Teyla, and hints of Shep/Teyla.

Notes: For the romantic pairings, watching Atlantis has made me see hints of both Sheppard and Weir along with Sheppard and Teyla. However, I don't really see anything between Sheppard and McKay except a deep friendship that is almost best friends. Both make fun of each other, poke fun, and generally will support each other, but nothing that would indicate any romantic feelings as I have seen in many Atlantis fanfics. I also definitely see something between Ronon and Teyla…^_^ Also, this is not my first time writing for the Stargate universe, but I've pretty much never published any of those works…

Story:

Chapter 1 – Mission

He should have known that the word routine was usually a sign that their mission was going to go downhill and roll into a giant pile of shit, but no, did he ever listen to that voice whispering in his head? John Sheppard grunted in pain as a meaty fist dug into his already broken lower ribs one more time and blearily tried to keep his eyes open. He saw vague shapes of people surrounding him, but he knew who they were ever since his team's capture on M3R-154.

Every fiber of his being was in pain and while some others were more acute, it still hurt each time pressure was put on. His hands and arms were already numb with both pain and loss of circulation, being held up behind him in a spread-eagle style. His feet, thankfully, were still firmly on the ground and thus, he didn't have to wrench his shoulders anymore than they were already.

One, he knew was already dislocated and his efforts in popping that joint back into its socket was rewarded by him passing out as soon as he felt it pop back in. He had only awakened to the rough shaking of guards hauling him up from his cell and to this torture chamber.

Well, at least the one bright spot in all of this was that there was no Wraith to feed on him this time around.

A damp trickle of sour tasting water touched his lips and startled him from his dazed thoughts as he jerked involuntarily against his chains. He gritted his teeth and suppressed the hiss of pain that coursed throughout his whole body as it reacted to his jerk. Glancing through one good eye, albeit a bit blurry at times he saw the grinning face of his captor and the tiniest tremor of fear shot through him.

He recognized the man in front of him.

The face that he had sworn to kill the next time they met…Acastus Kolya.

"Colonel Sheppard," Kolya smirked at him and John Sheppard knew that he was in deep trouble.

72 hours before…

"I'm just saying, couldn't we just stay for a couple more days?" John pretended to ignore McKay's whining and continued to trudge through the heavy underbrush that was on M3R-154. But he did let a small grin quirk the corner of his lips as he knew the real reason why Rodney wanted to stay.

In the small village they had encountered, the locals spoke of a powerful device that was used in ancient times to help defend themselves against the Wraith. But since all of the ancestors were gone, they didn't have anyone who could operate the device. Meaning…Rodney wanted to test the device using his own ATA gene. During their stay for the last few days, the scientist had all but set up camp in the room where the device was while he and Teyla were negotiating a treaty and trade agreements with the locals.

McKay wanted him to stand in the device to see if it would work with his gene, but he had declined with his usual faint grin and said that he would scout out the perimeter to see if there was anything else.

The real reason why he didn't want anything to do with that device was because it gave him the creeps. He didn't know what it was, but something about it made him feel uneasy. He had told McKay this, but the scientist practically ignored him and muttered something about how every soldier felt uneasy with things they didn't know.

"McKay, we can send in another team after we report back to Elizabeth," John said in a patient voice.

"But, the device…it's just waiting to be activated! I don't even know why you couldn't stand in the circle," Rodney complained, "would it have hurt you?"

"I don't really know," he turned back to look at his teammate, "besides, the thing gave me the creeps."

"Oh well sorry," the scientist grumbled, "I'm sure if we send in a lot more troops, scare the locals, and then you'll feel safer, is that it?"

John decided to ignore the last retort and turned back around, keeping his senses focused as they moved through the underbrush and back to the gate. There were times his best friend could infuriate him…and this was one of them.

"I'm sure Colonel Sheppard has his reasons, Rodney," Teyla's soothing voice spoke to his left.

"Yes, and they involve paranoia," McKay shot back none too loudly.

John tightened his grip on his P-90 and wished that he would shut up just as they came to the clearing where the stargate was located.

"Oh, we're here already," McKay commented, "that didn't seem as bad as the first time."

John had to agree with the scientist as he started to dial the address home. Their first time trudging through the underbrush was like trying to weed-whack the rainforest. Luckily the locals had some antiseptic and bandages for the numerous cuts they received. He knew that Dr. Beckett would have to look them over to make sure none of the antiseptic was harmful, but John didn't think so and knew that the good doctor would love to get his hands on some of what the locals had.

"Yes, and we did not receive many cuts and scrapes as before," Teyla agreed, punching in her IDC code before they all headed towards the gate.

Rodney was already going through the gate along with Teyla and he started to follow her lead when he turned around to see Ronon staring around at the clearing. Sheppard paused, wondering what the Satedan was doing.

"Ronon?" he asked.

"There's something not right," Ronon muttered, looking around some more, his eyes narrowed. After a few seconds, he shrugged and turned to face him.

"You okay?"

"I will be once we're off this planet," the Satedan replied as the two of them stepped through the event horizon and back to Atlantis.

A lone figure with haunted glowing yellow eyes watched them before it whistled a strange set of sounds. The figure stood up from the underbrush, its cat-like features riddled with twigs and bits of grass from lying so long in its position. Another set of whistles sounded from the distance before the cat-like creature sprinted away from the stargate, headed deeper into the woods.

Rodney resisted the urge to bounce excitedly in his seat as Carson was looking him over and taking a blood sample to make sure that the antiseptic that the natives had used on M3R-154 wasn't carrying anything harmful to the expedition or to themselves. All he wanted to do was to go back and keep examining the Ancient defense device. He still didn't understand why both Sheppard and Ronon were so uneasy throughout the whole mission. He didn't feel a damn thing and he had the ATA gene too! Even Teyla was taken in by the natives and was smiling happily throughout their whole stay.

Still…

"Can I please go?" he asked Carson who was finally took the damn needle out of his arm. He hated needles and didn't know why the doctor insisted on taking at least six vials.

"Yes, yes, yes," Carson shook his head, "you can go laddie." With the final snap of the tourniquet taken off, Rodney hopped off the table and walked quickly from the infirmary, headed straight to Dr. Weir's office.

He didn't bother apologizing to anyone who was in his way as he barreled down the halls, and burst into Elizabeth's office, a huge grin on his face.

"Rodney, you're early," Elizabeth tilted her head, a smile coming to her lips.

"I know, I know," his grin grew wider, "how about we just send another team back? I mean come on there's so much to do on that planet! I've almost got the device working again and it just needs a bit of tweaking-"

"Whoa, slow down Rodney," Elizabeth interrupted his line of thought with a hand and he blinked a few times in surprise then realized that she didn't know what had happened on the planet for the past few days. Even though Sheppard surely had reported in he figured that the man didn't report everything in.

"Oh, the Colonel didn't tell you about the device? No? Well then, it's an Ancient defense system that I think, from what my notes," he brought out his datapad and tapped a few buttons – those Ancient tracking devices were handy as mini notebooks too since his laptop was still sitting in his backpack which was in the nearby conference room but who cared where it was for now- "that we can get this operational and probably figure out if it has drones we can use since the tower defense system on MX2-334 is one source of the drones but we kind of need more when the Wraith discover that we're not all that dead-"

"Rodney…"

"-so anyways, this new defense system is activated as usual by the ATA gene and I'm on the verge of figuring out its codes and what it actually does to defend the place. But Sheppard, Teyla, and Ronon have been scouting out the place and the natives say that long ago the cullings have never happened. Only when the last of those with the ATA gene had disappeared that the Wraith showed up on their door step. The library's really vague-"

"Rodney…"

"-on how the defense systems actually work-"

"Rodney!" he jumped at the mention of his name and looked at Elizabeth who was shaking her head, a crooked smile on her face.

"What?" he asked, confused.

"Can you wait a few minutes more so you can tell me about the defense system during the briefing?"

"Oh…um sure," he blinked owlishly then shrugged and shut off the datapad before going into the adjacent conference room and sat down on one of the chairs. He missed the blossoming of a full smile on Elizabeth's face as she shook her head at his antics.

Elizabeth watched Rodney sit down at the conference table and take out his laptop. His whole posture was that of a giddy child wanting to go play in the sandbox and she suppressed a quiet laugh that threatened to come out of her.

The noise of the rest of the team coming in for their post-mission briefing made her glance towards the lower stairs where John, Teyla, and Ronon were climbing up to get to the conference room. A concerned look washed over her face as she saw that both men's postures were a bit tense while Teyla looked relaxed. Why were John and Ronon tense? Had something happened on the planet that Rodney and Teyla didn't know about?

Deciding to probe later, she got up and gathered the papers relevant to M3R-154. Walking towards the conference room she took her seat in one of the chairs, noting that the Canadian astrophysicist was mumbling about something and hastily typing away on his laptop.

A few seconds later the rest of the team came in and the door-like panes of the conference room automatically shut, sensing that a briefing was about to happen. Elizabeth still marveled at how sentient and life-like Atlantis was, sensing the needs of the expedition and making sure that in all possible ways, no one was hurt, save for the few times they knocked over experiments, jury-rigged Earth's systems to Atlantis…

"Rodney was explaining to me that M3R-154 had an Ancient defense system-"

"And we should go back because it needs to be studied," the scientist's voice took on a sing-song tone of annoyance.

"-what else have you found on the planet?"

"Habitable, peaceful traders…there's a total of about six other villages within walking distance of the main one, which looks like a capital city of sorts, though with wooden huts…" John shrugged.

"Too quiet," Ronon added his two cents in.

"They are fair traders and they do have medicinal herbs that may be useful to Dr. Beckett. They treated our wounds when we were walking towards their settlement," Teyla explained in a calm voice. She always ended up surprising Elizabeth with her motherly tone of voice and her ability to keep tensions from rising – it was one of the things that made her respect the leader of the Athosians so much.

"Wounds?" Elizabeth didn't like hearing that her teams were getting injured almost every time they went through the gate.

"Small wounds, Dr. Weir. Scratches and cuts we received going through the thick underbrush that surrounds all seven villages. I believe that it is part of the defense system, though more natural, to hold off the Wraith for a while," Teyla reassured her.

"I see," she nodded, sitting back before turning to her chief scientist, "so Rodney, what can you tell me about the defense system?"

"It's ATA gene activated, though since it hasn't been used for a while, I don't know if the system will recognize the ATA genes in ourselves, but I've been trying to figure out how it works and I think there might be an underground complex beneath this thing that probably would have a lot of drones that we can salvage for Atlantis to use against the Wraith or even the Asurans," Rodney turned his laptop around to show her the screen, "see? The systems are in Ancient, but I've been so far, been able to translate about a quarter of it."

"What does it say?" she vaguely recognized some of the Ancient text on his computer.

"It's like reading a poem, but I think it says that the device was left as a gift to the people of the village and something about Klisa'nthus, I've never encountered a word like that – anyways, being guardians when the time comes to defeat the Awakened Ones," Rodney shoved his laptop over to her and she took it, clicking on a few select parts of the text.

"Awakened Ones?" she asked.

"Most likely the Wraith," Teyla replied, "we did see a few Wraith corpses scattered in the underbrush, though most were heavily decayed."

"Klisa'nthus?" she asked, her eyes scanning over the text. Though she wasn't as literate to translate the text like Dr. Jackson was back on Earth, she still was able to pick out a few words. "Rodney, can I have a copy of this text?"

"Sure, sure," the scientist nodded absently.

"We were not able to find any reference to whom or what they were, though the village's ancient texts do mention them," Teyla replied.

"And what did they do in those texts?" she asked, glancing up to look at the team.

"Kill a bunch of Wraiths during a few cullings…I get the feeling that they live for a very long time," John shrugged again and Elizabeth noticed that the tension in his body still hadn't gone away.

"Was there anything wrong?" she probed.

"No…not really…it's just that I don't like that defense system. You know I'm not the one to be scared of anything," he waved his hand in a vague direction, "but this thing gives me the creeps."

"Me too," Ronon chimed in. The large Satedan rarely took a seat during the post or pre-mission briefings and even now, he was standing behind John and Teyla, his arms crossed over his chest, resting against the wall.

"The creeps?" she raised an eyebrow. In the three years she had spent in Atlantis, she had rarely seen John concerned or scared of anything, and even those few times, he had kept a firm mask on his inner emotions, choosing only to display a mask of nonchalance and distant concern. But Elizabeth had seen those few times he was truly scared, angry, or concerned.

So for him to admit that he was worried about the defense system made her concerned. While Ronon was naturally suspicious of anything and everything, she was learning how to read his emotions through his voice and posture; it was what made her such a great diplomat and help negotiate almost impossible treaties.

"I don't know, but I just don't like it-"

"Of course you don't like it Colonel; we don't know anything about it," Rodney snipped from his end of the circular table.

"McKay…" John's tone took on that of annoyance.

"Gentlemen," Elizabeth held her hands up towards both of them to stop them from launching into one of their regular snipping wars with each other. "Please. Now, John, why don't you like it?"

Her military commander shifted slightly in his seat for a few seconds, trying to gather his thoughts and Elizabeth felt a flash of sympathy for him. She knew that he didn't like to express his feelings when it involved certain things and most of all, didn't like to express weakness in front of others. This was probably one of those times.

"It's…just a bad feeling. Like something's bad was going to happen if we stayed there any longer…I dunno."

"It feels more sinister than the Wraith," Ronon supplied and Elizabeth stared at him, surprised.

"Sinister than the Wraith?" she glanced at Teyla who shook her head, confused.

"Oh please, sinister than the Wraith…what can be more sinister than life-sucking aliens?" Rodney shook his head.

"I didn't feel anything of the sort," Teyla knew that she was asking about her Wraith-sense.

"Come on…can I please just go back and study the thing?" she glanced at her chief scientist.

"I don't know…if both Ronon and Colonel Sheppard have bad feelings about this-"

"Elizabeth," though she never showed it, it really irked her to hear her name being dragged out like that as if she was a small child. "Sheppard and Ronon can stay here. Send Major Lorne and two units of Marines with me if you're so worried!"

She glanced over to John and to Ronon. Ronon just shrugged, clearly indicating that he would rather stay in the city than go back to the place. John stayed quiet for a few seconds before sighing softly.

"I guess if McKay wants to go back have fun with his experiments-"the first sign that the tension was leaving was a crooked smile to Rodney who was rolling his eyes, "then Lorne and two teams should be fine."

"All right. You have a go Rodney," she turned to her chief scientist who looked absolutely ecstatic and was grinning from ear to ear, "but, first sign of trouble and you're heading back."

"May I go with Dr. McKay, Dr. Weir?" Teyla spoke up, "the locals had some things I think my people would like to trade with them and plus I may be able to bring back more herbal medicines for Dr. Beckett to study."

"Yes, that will be fine," she nodded, "you'll be leaving tomorrow at oh-nine-hundred providing Dr. Beckett clears you."

"Good, good," Rodney started to get up, rubbing his hands gleefully, "now I need to get some supplies and stuff…"

The others took it as a cue that their briefing was over, besides writing up mission reports and the door-panes opened up, revealing the hustle and bustle that was the hub of the control room of Atlantis.

"John, can I see you in my office for a few minutes?" she called after him and he nodded, changing his direction to head to her office after telling Ronon and Teyla that he would join them for lunch in a few minutes.

She gathered her papers and headed into her office before taking a seat in front of her desk. John was already sitting in the chair in front on the opposite side of her desk, staring out at the view she had of the gateroom, a distant frown on his face.

"What's bothering you, Colonel?" she asked, bringing his gaze towards her. She noticed that while he seemed a little more relaxed, there were still tension lines around his eyes.

"Nothing much," he shrugged.

"John," she smiled slightly, "I know you better than this. You're worried. So tell me what's bothering you that you didn't want to say in front of the others during the briefing?"

He fidgeted in his seat for a few seconds, before he looked up at her, "Something just doesn't feel right on that planet, more so near the device than anything else."

"Ronon said it was more sinister than the Wraith…did you get that feeling too?" she asked gently.

"No," he shook his head and became quiet for a few more minutes his gaze turning towards the gateroom once more, "I just had the feeling that we were being watched…"

"By the natives?"

"No," he shook his head before sitting up from his seat and holding his hands out, "you know that feeling like someone's analyzing you?"

"Yes," Elizabeth had that feeling lots of times during her negotiations.

"It's like that…but somehow different," John scratched the back of his head.

"Should I tell Rodney to postpone the mission?" if this was something that was really bothering John, she knew that she should stop the return mission before anything else happened.

"No…let him go for now," John shook his head, "just…tell Lorne to be extra careful, all right?"

She nodded, "All right."

"Good," he slapped his hands on his thighs and got up, "now if you'll excuse me. I'm gonna get some lunch."

She smiled as he got up. "Get some rest Colonel."

He returned the smile before walking out of her office and towards the mess hall. She watched him go, a feeling of worry running through her. He had been through so much and yet, seemed to bounce back with more vigor than ever. She knew that he kept his innermost feelings hidden from others and though she didn't prod at that part, she wished that he didn't have to keep it bottled up inside and instead opened to at least someone so that the pain, guilt, anger, and whatever else was wracking him wouldn't eat him alive.

She had recommended he talk with Dr. Kate Heightmeyer, but even the psychologist's efforts to get him to open up was at a dead end. The rare times she had seen his true emotions had always left her half-scared, half-relieved…and many of those times, she realized, was when she was in mortal danger.

Teyla had told her when they were just talking one day, that John had reluctantly confided in her that he considered, herself, Teyla, Ronon, McKay, Zelenka, Lorne, and even Ford his family. Though she knew that the full conversation between her and John was in confidence, she still appreciated that the Athosian told her a part of it.

She just hoped one day he would be able to trust all of them enough to show his true feelings instead of hiding under his mask all the time.

Even with a full and satisfied stomach that had been growling slightly during the few days they were on M3R-154; partially because of the slightly inedible food the natives served, John stared up at the ceiling that was his quarters on Atlantis. Night had long fallen on the city and while lunch and dinner were mildly funny, especially with Ronon still not quite used to all of Earth foods, he still couldn't get to sleep.

Beckett had cleared all of them from the blood work he had done and was positively excited about the sampling of medicine that Teyla had brought back and had been buried in his lab for hours until he was literally dragged into the mess hall for a late dinner by one of his staff members. McKay then proceeded to needle the doctor for not eating healthy and insisting that they all do and it was a nice verbal battle going on between the two that John didn't feel like interrupting.

Still…he glanced lifted his wrist and pushed the glow-setting on his watch and the clock showed that it was roughly one in the morning. Thankfully, Atlantis seemed to have a 24-hour a day time clock and so everything was corresponded to that. He didn't know what was bothering him – check that, he did know, but couldn't quite put his finger on it.

It was the damned defense system device that McKay was going on about for the past few days. It scared him and he didn't like things that scared him. Okay, the Wraith were scary, but he was more pissed at them than scared. He knew that he hadn't been totally truthful to Elizabeth during the post-mission debriefing, but it wasn't anything that was going to threaten McKay on his return trip back. It was just that the thing made him feel cold inside, a sense of inevitable doom. Ronon had said that it felt worst than the Wraith and right now, he was inclined to agree with the Satedan.

However, he guessed that either McKay was too caught up in exploring the device or was immune to its effects. Teyla was probably immune due to the Wraith gene she had within her. But the odd thing was that it was almost like a gut feeling, and he usually trusted his gut feelings, even though it sometimes it ended him up in trouble.

Turning over to a more comfortable position on his bed, he forced himself to relax and closed his eyes. Hopefully McKay would be able to get something useful out of the device so they can all just leave it alone afterwards. An uneasy sleep drifted over him and somewhere in the back of his mind, John knew that something terrible was going to happen…