A/N: My first serious Atlantis fic! This started out as a conversation I was having online with Mary Christmas about hurt/comfort fics in general and after I had signed off, I began plotting and came up with this. It is a WIP, so updates may be slow. I am looking for a beta-reader if anybody's interested.

"Darkness of the Soul"

Chapter One

Pain.

All Elizabeth knew was pain, pounding in her skull, racing along her nerve endings. She gasped as her mind slowly gained consciousness and wished she had remained oblivious. She had never felt anything as agonizing as this; nevertheless, she struggled to push it to the back of her mind where she could ignore it, to focus on her surroundings.

It was a long, weary fight, but by remaining still, the pain eventually subsided into a dull, aching throb. As long as she didn't try to move, she would manage.

Carefully, she opened her eyes a crack. When she wasn't immediately blinded by light, she opened them further to find herself staring up at a high beamed ceiling of some sort, though she couldn't really tell what it was in the semi-dark. Confusion and disorientation fought alongside each other as she attempted to determine where she was at, and how she had gotten there.

Squeezing her eyes shut as a fresh wave of pain surged through her, she tried to remember what had happened last. Bits of memories flashed past her mind's eye. Flowers. Gunfire. Teyla being grabbed. Darkness.

She gasped and her eyes flew open, concern now filling her. Had that all really happened, or was she just imagining things? Slowly, she sat up, wincing with the sharp jab that lanced through her head and steadying herself against the sudden dizzyness. Her pain-clouded eyes took in the musty surroundings.

It was an enormous, one room building and she was at the end furthest from the door. Though it was now empty, save for herself, there were pallets of furs similar to the ones she was laying on spread about in a seemingly haphazard way. The only lightsource she could determine was the various cracks in the walls, letting sunlight filter through.

Unfortunately, her observations didn't tell her any more than what she already knew and she lay back on her own pallet. Taking a deep breath, she tried to recall everything she had done since she had woken that morning. She had no way of knowing if it was the same day or not, but that could wait until later.

Closing her eyes, she let her mind drift until a memory snagged it..

--Flashback--

It was very early when a knock on the door of her quarters woke her up. Elizabeth frowned, sleepily crawled out from between the warm blankets, and stumbled over to the door. When she opened it, she practically cursed to see Rodney standing there, his hand raised to knock again.

He must have sensed her bad mood, because he began apologizing profusely, something he rarely--okay pretty much never--did. She frowned at him and waved him off.

"What is it, Rodney?" she asked snappishly.

"What is what?" He sounded distracted and had an odd expression on his face as he stared at her.

It was too early for this. Either that or it was just going to be one of those days. Whatever the reason, Elizabeth lost her temper. "Someone had better be dying, Rodney," she growled, before she could keep the words back, "Or you're going to find yourself put on the remotest, barronest planet I can find."

The astrophysicist blinked at her and then walked away, mumbling something about it not being that important, sorry for waking you. Elizabeth sighed, instantly contrite. It wasn't his fault she hadn't had much sleep in the past week. She'd have to go find him and apologize.

After she found some coffee.

Later that morning, she sat in her customary chair at the conference table. Sheppard and Teyla were the only others in the room, and they were talking in quiet voices with each other. Elizabeth smiled slightly, but didn't comment. Her mind was still on her confrontation with Rodney earlier. She hadn't been able to locate him once she'd had her coffee and began to think the man was avoiding her on purpose.

Just what she needed. A guilt trip.

She sighed just as Rodney and Ford walked in. The young lieutenant took his own seat, but Rodney gave her a quick, indecipherable look before sitting in the chair furthest away and refused to look at her again. This hurt her for some unacountable reason, but she pushed the feeling aside. She'd catch him after the briefing and apologize then.

"All right," she said, and they all turned their attention to her, "Teyla, the Athosians still haven't managed to figure out why the crops aren't growing as they should?"

"Correct," the Athosian woman said, "It may be that the soil is not quite the same as what we are used to, but Halling says they should have been able to counteract that."

"All right," Elizabeth murmured, "Well, we need food. The stores have just about been depleted, and unless we find something soon..."

She let her voice trail off there, knowing they'd understand what she meant.

Rodney was uncharacteristically silent, and Elizabeth chanced a look at him. He still wasn't looking at her, but a frown had creased his brow, as though he were thinking of something.

"Doctor McKay, do you have something to add."

The scientist looked up as though scalded, opened his mouth, closed it and shook his head. Elizabeth frowned, but didn't press him.

"I know of someone who may trade with us," Teyla began tentatively, "But I have never met them. My father and Halling have always done the trading." Her face was also creased in a frown, but she went on, "Even after my father's death, Halling or another male have always done so, when necessary."

Again, Rodney opened his mouth to say something, but he glanced at Elizabeth first and shut it quickly. Sheppard seemed to have noticed this too, because he kept looking at McKay as though he had grown a second head.

"We could always send Halling to speak with them," Ford said, "Right?" The young man asked the last of Elizabeth.

"Sure," Sheppard said before she could respond, "But I think we need to do this ourselves. We need more allies."

The last was said with a hint of bitterness, and a look at all the faces showed they were all thinking of the Genii, and the Hoffans. Races that had been nearly as advance as they were, but who had used them to further their own means.

"And I suppose we're just going to go up to them and say 'hi', right?" McKay finally said and Elizabeth felt herself relaxing ever so slightly, "I mean that's what's been getting us into so much trouble, isn't it? They don't trust us."

"That's why I'll be going with you," Elizabeth surprised herself by saying.

Judging by the looks on the others' faces, they were all just as startled by the statement. However, it felt right. She was, after all, a diplomat. Keeping the peace between the people of the Atlantis base was one thing, but she yearned to actually go out and meet peoples of other cultures. The one time she'd had any dealing with aliens was when she had bluffed the System Lord representatives into leaving Earth (and their possible weapon) alone.

Once Sheppard had recovered from the shock, he began to immediately protest, Ford right behind him.

"It's too dangerous."

"If we make first contact, then you can..."

"...meet with the alien leaders."

"We just need to..."

"...make certain they're not..."

"...hostile."

Elizabeth blinked and looked between the two of them. They looked at each other and then burst out laughing.

"I knew I shouldn't have let you read Harry Potter," Rodney said testily.

"What is Harry Potter?" Teyla asked.

"It's a series of books about a young boy who can do magic," Elizabeth interjected before any of the men could say anything, "And it's not the issue here. I appreciate your concern, gentelmen, but I am going. That's final."

It wasn't final though, and they spent a good deal of time arguing about her safety, and her importance to Atlantis. Rodney and Teyla remained silent throughout, watching the three of them as though it were interesting entertainment.

Finally, Sheppard reluctantly agreed, though Ford still seemed uncertain. The Lieutenant wouldn't go against his commanding officer though, so Elizabeth was smug in the face of her triumph.

As they all gathered their things to leave, she stopped Rodney and indicated she wanted him to remain behind. He gave an annoyed sigh, but he did as asked anyway--even though he had resumed studiously not looking at her.

"I'm sorry for earlier," she told him softly, "I guess I'm not much of a morning person, but it's no excuse for being so...surly."

He blinked and looked at her incredulously. "I thought that you were angry because...oh never mind. I've got to go make sure Carson hasn't stolen my supply of cheese curls, and then make sure all the equipment on the Puddle Jumper is in order before we embark."

Elizabeth watched him as he practically skipped from the room and shook her head. At least he wasn't being sullen any longer. Then she began her own preparations for the coming mission.

-----------

The planet they 'gated to was lovely. Devinely scented flowers grew up over nearly every surface--rock, gravel, trees--and were overpowering in their intensity. Elizabeth was delighted. It was the first time she'd set foot through the 'gate since coming to the Pegasus galaxy and this was a very good omen.

At least it was until Rodney mentioned something about the Garden of Eden.

"Good thing none of us have allergies," Sheppard commented loudly, to cover up McKay's words, "'cause we'd be having a really hard time of it."

"Yes, sir," Ford said with a grin, looking around with relish.

"Father never told me how beautiful this place was," Teyla said in awe, "I wonder why he wouldn't let me come."

"Probably because this is one of the Wraith's first stops," Rodney said. Of all of them, he seemed to be the only one not enjoying the scenery. Of course, that was normal for the acerbic astrophysicist.

"Try to be a little more pessimistic, McKay," Sheppared muttered, "I don't think anyone's convinced yet."

Before Rodney could retort, the sound of heavy gunfire distracted him. Instantly, Sheppard and Ford were on the alert, with Sheppard glaring at Elizabeth as if to say 'See? I told you it was too dangerous'.

"Get down," was what he said aloud, however, and Elizabeth dropped to the ground with Teyla and Rodney on either side of her.

Ford crawled over to them, and raised to a half-crouch with his gun pointed towards where the weapons fire could be heard. Suddenly, it stopped, and the only sounds Elizabeth could discern were her heartbeat and breathing. The rest of the clearing was eerily silent, and she marveled at the way she hadn't even realized that there had been some birds and small animals.

After a few minutes, Sheppard relaxed. Ford continued to keep his gaze trained on the dense forest. Elizabeth rose slowly and turned towards Teyla, only to scream in fright. A strange creature covered in mismatched fur had a hold of the Athosian woman.

Elizabeth surged towards it, as Ford and Sheppard turned towards her. She could hear them shouting a warning, but it didn't register in her brain. The next thing she knew, she felt a sharp pain in her leg and in her head. Then everything went black.

---End Flashback---

Elizabeth jerked awake as she felt something soft and cool touch her face. She opened her eyes to see a young woman who could be no older than Ford kneeling at her side, dark eyes filled with concern. At least the pain wasn't so bad this time. She felt that she would actually be able to move if she were careful enough.

Testing out her theory, she slowly sat up. No pain. She smiled and looked at the young woman again. Then she did a double take. The girl was wearing nothing but a shift and it made her aware that she was wearing something similar.

"What is..." she began, but the girl quickly placed her hand across her mouth.

Elizabeth glared, but was too weak to get away.

The girl frowned slightly and then bent to speak softly into her ear. "No speaking allowed. They'll hurt us if they hear us."

Then she was gone, leaving Elizabeth alone to ponder on her situation. Where was Teyla? Were the others all right? What had happened? And who were the 'they' that girl was talking about?

tbc

A/N: Yay! Here's chappie two of my chaptered story. And I now have a betareader! Thanks so much Judith. Of course, any mistakes are mine and mine alone.

The nauseating stench of blood and burnt flesh filled the air, and Aiden Ford choked as his mind slowly became conscious. He opened his eyes and found himself staring at an unrecognizable charred mass, causing his stomach to rebel. Sitting up slightly, he brought up his breakfast, gagging aswhen the retching began to produceing only dry heaves. Finally, he was able to catch his breath, and wipinged his mouth with the back of his hand, and swallowing against the acidic taste left by the recently ejected bile left.

Steeling himself against a second sight, he pulled himself up and sat cross-legged on the ground, waiting for the as a wave of dizziness to pass, and so he could take took stock of his situation and environment. The latter was easy to determine. He was in the middle of a forest, with sunlight filtering down through the leaves. The muted lighting coupled with the absolute silence and the...thing, lent an eerie eery, surreal quality to the air, and Aiden couldn't stop the small chill that ran down his spine.

His situation was a little harder to determine. A quick check of his person revealed that his side-arm, P-90 and other weapons were nowhere in sight, and his radio were was also missing. He still had a few MRE's and his canteen was full, so whoever had taken the rest of his equipment either hadn't realized what they were, hadn't found them interesting enough to take, or simply hadn't wanted him to die immediately. Of course, none of that explained what he was doing here in the first place. He closed his eyes and concentrated.

He remembered running after the beasts that had carried off Teyla and Dr. Weir off, remembered Major Sheppard's order for them to retreat as more of the creatures began attacking en masse. They had fallen back to the Puddle Jumper, and as quickly as they had come, the things had gone. Then, McKay had mentioned picking up a strong energy surge coming from the direction the two women had taken...and... Everything else was a blur. He remembered being Being attacked again. Gunfire, screams of pain...then flames.

And people's voices...men's voices.

He shook his head to see if that would help, but all it did was make him dizzier. His head sunk into his hands and he sagged, feeling depleted of energy.

'Okay, brief moment of self-pity over, Aiden,' he told himself, 'time to figure out what's going on.' With a deep breath, he got to his feet and glanced around. But with no compass, and no way of knowing which way the 'gate lay, even if he had had one and it had worked on another planet that wasn't Earth, he was pretty much...lost.

So, until he could get his bearings, he turned his attention to the... thing, taking it in this time with the eye of a soldier. Though it was misshapen, it was undeniably one of the beasts. A long, burnt stick, that he hadn't been able to see from sitting, lay on its other side. A torch. And it would explain why he remembered flames.

But who, or what had made it? And why had they left him here in the forest? More importantly, where was everyone else at? Major Sheppard and McKay? Dr. Weir and Teyla? He bit his lip and looked more closely at the signs left behind. He could see where many feet had trampled through the foliage, breaking tender new growth and dead leaves beneath. That and the fact that the smell of blood was so fresh, led him to believe that whatever had happened, hadn't been long ago.

"Well," he said aloud, "There's nothing for it but to go." He began following the path left behind by whoever had killed the beast.

----------------------------

Aiden leaned back against the large boulder, ignoring the jagged edges that bit into his back and gazed up at the sheer cliff in despondence. While he had excelled in rock climbing, even as a kid, he knew that this would be all but impossible to climb, even if had the proper tools. And though there could possibly be another way around, if he were to follow the cliff, the trail he'd been following ended here. Abruptly.

He pulled out the canteen, unscrewed the cap, and took a sip, swirling the water around in his mouth before spitting it out. Then he took a larger drink before capping it and replacing it on his belt. The refreshing coolness did nothing to clear his head, or bring about an epiphany, though it did help that his mouth no longer tasted as though something had crawled into it and died.

"Damn it!" he shouted, bringing his fisted hands forward and then banging them back against the boulder in a fit of pique.

But his left hand met with no resistance, and sank into the rock. He blinked in surprise as the cliff face began to shimmer, then disappeared entirely, revealing a long, dark tunnel. He grinned and muttered, "tThat's more like it."

Wafts of cool air drifted out of the tunnel, and Aiden cautiously walked towards it, his grin fading as he realized something. Whoever had built this complex security system had to be extremely advanced, but the people he had been following couldn't be, as evidenced by the torch and burnt carcass. He didn't know what that meant, at the moment, but knew it was important and filed it away to look at later, when he had more information.

His mouth tightened and he took a hesitant step inside. Nothing happened, and then he was all the way inside and there was a strange whine to the air. The tunnel was plunged into complete darkness for a second, before the artificial lighting he had become used to on Atlantis kicked in.

So it was Ancient design. The idea he'd had clicked into place. McKay had said something about a power surge. Could it have been the deactivation of the hologram? Or something else that was related?

Somewhere he had read something about not jumping to conclusions without all the facts. Well, in order to get all the facts, he'd need to investigate further. All signs seemed to point in this direction, so he'd take it, and he'd manage, come what may.

tbc...