Stargate: Atlantis; The Alternate First Season

By WeaverOfDreams777

Rating: PG-PG13

Genre:Action/Adventure

Disclaimer: I do not own Stargate:SG1 or Stargate:Atlantis.

Warning: This story is not meant to fit the storyline set forth by the producers of Stargate. It is AU, Alternate Universe. If you don't like that, don't review. You don't have to read it.

In the premier episode of Stargate:Atlantis, the Atlantis team awakened the Wraith. Major John Sheppard feared he may have made a mistake when he tried to rescue the captives the Wraith had taken. When he killed the blue witchy Wraith chick, he awakened the rest, and made it look rather like the beehive of doom. Two or three Wraith tried to follow him through the stargate into Atlantis, but to put it nicely, they were unsuccessful.

Chapter one: And So It Begins

The thudding sounds the Wraith ships had made as they had struck the shield of the stargate were still fresh in his mind. He had cut it almost too close. Wier was giving him the eye too, so he knew he was in for it. Once the former captives were running around Atlantis in relative safety, Wier took him aside. As she turned to him to let him have it, she turned into a Wraith.

Maj. John Sheppard woke with a start. He rolled his eyes as he realized he had fallen asleep in a chair slumped over one of the cryptic consoles the Ancients had vacated. He'd heard something, he knew it. The stargate had powered up, and was swirling mystically. He guessed he must have bumped a switch or something, and tried to find it to turn it off, yawning. He knew the pessemistic techies would have his head if they found out he'd powered up the stargate. He found the the switch he'd bumped and tried to turn it off. It didn't work.

Something was overriding the controls. He blinked. Nah, he just wasn't pushing the right button, he was just overtired. Suddenly, a face appeared through the whirling blue stargate, then a person followed the face. And another, and another, and another, five people came through the stargate. Clearly, he had to be dreaming, or seeing things. Maybe Dr. Weir had drugged him or something. Yeah, that was it, a hallucinogenic drug. He was nodding to himself when the five robed people began to approach him. He reasoned that they couldn't really be there, because the controls in front of him weren't working, so he couldn't have let them in even if Wier had authorized it. A tall male with long, straight, golden hair walked gravely up to him, followed by a male with loosely curly dark hair. The curly haired one looked odd, his hair had the wierdest reddish tint to it. Another male, taller than the previous two, with skin like polished ebony, approached another console and waved his hand over it, shutting down the stargate.

Two females were bending over the sleeping guards. One had golden hair and very pale skin, the other had black hair and skin the color of caramel. John's eyes were drawn to the darker woman, her dress was such a vivid red, redder than he'd ever seen a fabric be. The dark haired male stooped beside him and reached under the console.

A few seconds later, John heard the dull hum of a generator kicking in. His attention was quickly diverted, and he looked to the males as they moved quietly through the room, flipping switches, pressing buttons, and doing essentially everything the techies had said that no one was allowed to do. John made no move to stop them, he had a feeling that all he could do was watch. The women were chattering to each other, stuffing pillows under the heads of those sacked out on the floor. Where they'd found the pillows, only heaven knows.

The ebony man touched John's shoulder.

"Come with me." rumbled his deep, distinctive voice.

John didn't dare argue. He followed the ebony man down a maze of passageways, losing track of time and direction.

"We are under the city. It has come to our attention that the generators that power the shield have failed. I shall show you how to repair them."

Dr. Weir heard footsteps by her head. She knew that everyone was asleep but the stargate guards, so what could it be? Her eye opened a slit. Her eye took in the fact that a train of rich, deep blue fabric was gliding by her. This one did not belong. She opened both eyes and looked up, she saw a man, standing beside where she lay, with his back to her. He had a panel of sort open, and was looking at a tangle of wires with deep concentration. She didn't think twice before hitting him over the head with a ratchet wrench one of the techies had left out.

He collapsed to the floor with a soft thump. Weir felt a a little guilty. She might have only knocked him out, and then again she might have mortally wounded him. Why she cared was beyond her. He had seemed so harmless though.

She knelt beside him and ran her fingers through the soft, loose curls on the back of his head, trying to make sure she hadn't broken his skull or anything of that nature. She had punctured his scalp. She felt silly for forgetting that the switch for reversing the direction of the wrench was on the side she'd clubbed him with. She took care of that, then got up to go to the stargate room. She looked back down at him and paused. She really should tie him up so he couldn't follow her. She tied his wrists and ankles, and stuffed a kerchief in his mouth for good measure. he wasn't going anywhere.

Five minutes later she came back to make sure he was still down for the count, and he was on his feet, trying to shake off the cobwebs. He looked surprised to see her. He staggered backward. Weir had a random thought that he probably considered her a crazy lady merely out to get him. She confirmed it by knocking him unconscious again with an uppercut to the lower jaw.

She heard a soft cry of dismay behind her and whirled. John was standing there with a hand to his mouth.

"Dr. Weir! Why did you do that to a non-aggressor? He wouldn't have hurt you."

"Major! Where have you been?! Where did this man come from?"

"Doctor, he belongs here. He's a physician, in fact. He wouldn't have done you or anyone else any harm. His name is Jerhun."

"What do you mean, 'he belongs here'? I did not bring him on the expedition."

The golden haired male walked up behind Major Sheppard. Weir's jaw dropped.

"I see you will be keeping Jerhun. It is well, he knows as well as I do how to repair the things here in the old city. He may be of help if you encounter the Wraith."

Dr. Weir looked doubtful.

"How will he be of help? Won't he just be wraith-fodder?"

The golden haired being smiled and shook his head.

"No, they generally leave Jerhun be. He gives them indigestion. He gets into their minds more than most."

"Thank you, Gonfalon. I'm on a need to know basis and that was something I did not need to know." John said flatly.

"Well that explains why I heard his thoughts...." Weir muttered.

Jerhun couldn't move, he was tied too tightly.

"Sorry pal, the witch herself said I couldn't untie you." a voice said softly.

Jerhun struggled to reach for the knot that dug into his wrist.

'Please! Let me go!' Major Sheppard heard it as clear as if it were spoken.

'Oh trust me, I'd love to, but you can't imagine the trouble I'd be in.' he thought.

'I can imagine, Major John Sheppard, how much trouble you would be in, but I see in your heart you don't usually strictly obey such orders anyway. You do as seemeth right unto you.'

'Get out of my head you wierdo! You don't belong there and you know it!'

'Who's to say I'm not the voice of your conscience? Or perhaps I am yourself, and you have a split personality.'

'Nah, I know my own "inner voices", and you sound different. Now get out of my head, Jerhun.'

'You are one of my kind, Major John Sheppard. You make it too easy for me to get into your head. You wish to communicate this way.'

'No, I'm not one of your kind. I've got some of the same genes as the Ancients, but I don't know what you are.'

'Who are the Ancients?'

'They're the race that built the stargates, and they built this city.'

'Major John Sheppard, if that is so, then I am one of the Ancients. As is Gonfalon, and Threx, and Siara, and also Caris.'

John whipped out a knief and started cutting Jerhun loose.

The young looking Ancient sat up unsteadilly.

"I shall remain out of your head from now on."

"Well thanks. I'm glad to hear that. So how can you be one of the Ancients? You're so young."

"Am I young?" Jerhun smirked. "Just how old do you think I am?"

"I don't know, perhaps twenty, maybe forty if your race ages slowly."

Jerhun grinned, looking away.

"I ache to be that young again. How old are you?"

Sheppard stiffened.

"I'd rather not talk about that."

Jerhun had been roughed up a bit in the past couple days, the lithe, graceful Ancient had an uncanny habit of suddenly appearing when you least wanted him around. Such as when Elizabeth Weir discussed his fate with John Sheppard. She was in favor of keeping Jerhun drugged and guarded, out of her way, while Sheppard thought that having him running loose was perfectly fine. Sheppard trusted him, Weir had a deepseated dislike for him. Weir rather thought of Jerhun as something to be studied, like a mammoth frozen in ice, while Sheppard thought of Jerhun as an equal who should be treated with great respect.

So far though, Weir had been the one who got her way. Jerhun had been drugged for hours the day before. He'd reacted poorly to the drug and been sick for quite a bit. Sheppard had been majorly aggravated by that, and 'abducted' Jerhun from Weir. Jerhun had spent the night wrapped in blankets and sleeping fitfully near the major. Several times, Jerhun had looked longingly toward the stargate, after seeing Weir.

Sheppard had dressed Jerhun up in battle gear this morning, he was taking him through the gate with him to explore one of the neighboring planets. Jerhun had an incredable capacity to remember things, and he remembered virtually everything anyone said, almost word for word.

Somehow, the question of Jerhun's age came up again. He confessed to Sheppard that he'd been about 19 when he was put into suspended animation by some of the Ancients, who thought him a deadly hybrid. Only about 10 years ago had he been awakened, by a mother grieving her lost son. She'd seen him and thought him so young, innocent, and worthy of being set free. He'd had a lot of trouble with being drugged since then. He didn't know how long he'd been in suspended animation, and no one was going to tell him. Some of his adoptive mother's neighbors had captured and drugged him, intending to put him back in stasis, but all they'd succeeded in was making him deathly ill.

"How are you a deadly hybrid?" Sheppard asked.

Jerhun lifted his eyes from his boots to Sheppard's face. For a moment, those pale cheeks hollowed, those intense eyes became sunken and dangerous, the long-fingered hands became clawed, and Sheppard's heart skipped a beat.

"I'm part Wraith." rasped the apparition.