Dark Conversion Chapter 1, a stargate: atlantis fanfic

Spoilers: through Season 2 episode "Instinct" (picks up right after it), commercials for "Conversion" and (only slightly) "The Lost Boys"

Author's Note: Italics signify thoughts or emphasis. One row of Xs is change of POV, two rows is change of scene.

Part 1 of 5.

This is my first attempt at a Stargate: Atlantis fic, so don't be too hard on me.I was challengedto write what I think could happen in the episode "Conversion" in which John Sheppard turns Wraith-buggy, but putting as dark a spin on it as possible (for me, anyway). If you've read anything of mine, you'd know I nearly always write happy fics, so it was quite the challenge (which I did ask for). Also, I am a die-hard ShepWeir shipper, so there will be a little of that reflected in here, though it is by no means a romance.

This was plotted out and mostly written before the actual episode, so it doesn't follow that storyline except for the fact that John is infected and mutating.

Warnings: Rating for violence, brief language, and character death. And just because I kill someone off in this fic DOES NOT mean I want them dead on the show.

Disclaimer: I don't own Stargate Atlantis or its characters, if I did Elizabeth would go off planet more often, and she and Shep would… well, you can guess. I also don't own a few short lines of dialogue that appeared in the commercial and episode.

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"Colonel Sheppard, you are injured," Teyla remarked when John and Ronon returned to her.

She had felt good enough to sit up only seconds before, and now Teyla allowed herself to be pulled to her feet by Ronon. Her head swam a bit, but she tamped down on the swell of dizziness and concentrated instead on being ready to move back to where Rodney and Carson were waiting with the villagers. She brushed stray bits of the forest floor off her pants and the back of her jacket, picking John's up off the ground where it had served as a cushion for her head. Teyla shook out the cloth, tucking it into the crook of her arm when John showed no inclination to take it back.

"It's just a scratch," John replied, surreptitiously wiping some of the blood off his forearm.

"And Ellia?" Teyla asked with a lift of her brows.

She'd heard the gunfire, and the creature that Ellia had become in her desperation to be human was not with the two men. Teyla's suspicions were confirmed when Ronon and John shared a glance before looking away.

With a soft sigh, she nodded, "I see. We must return to Dr. McKay and Dr. Beckett. The villagers will want to know they no longer have anything to fear from the monster in the forest. I am just relieved that Zaddik did not have to know the fate of his daughter."

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The walk back to where Rodney and Carson waited with the villagers was accomplished quickly and in silence. John was trying to ignore the slight burning sensation in the wound on his arm, thankful that it wasn't worse. He didn't understand why, but Ellia had apparently been unable to feed in the form resulting from Carson's serum. He didn't have a mirror on him, but he knew Ronon or Teyla would have said something if he looked any older or drained in any way.

Perhaps her inability to feed the way the Wraith did was why Ellia had cut into his arm. Maybe she had been trying to latch onto his arm in the way that bug had attached itself to his neck previously. Whatever the reason, Ronon had been right; Ellia had been too far gone, she never would have come back with them. With how many times he and Ronon had been forced to shoot her, John wasn't sure if even a Wraith stun weapon would have been enough.

"The Daemos in the woods will never bother you again," Ronon announced to the villagers when they reached the group.

Until the next culling, went unspoken. Why not let the people enjoy their lives while they could?

Sighs of relief and excited chatter followed the announcement, but Carson was not distracted from the fact that one of those under his care had been injured, nor did he forget about the potential use they could get from the deceased Wraith girl's body.

"Colonel, hold still," Carson commanded when John wouldn't let him inspect the wound in his arm. Out of hearing range of the villagers, he remarked, "We have no idea what Ellia could have done to you."

"I'm fine, Beckett," John bit off. "We need to get back to Atlantis and report in."

"What about the body?" Carson asked, finally relenting his hold on John's injured arm. "I need to find out what went wrong, why the serum stripped the human genes instead of those of the Iratus bug."

"We'll send Major Lorne's team back for it," John decided aloud. "Teyla and I are both injured, you and McKay need to carry the equipment back to the 'gate, and I'm pretty sure Ronon would rather have a bonfire with it than carry the body anywhere."

"Aye," Carson replied. "I suppose that's best. Excuse me, Colonel."

The Scottish doctor made his way to Teyla's side to tend to the wound on the back of her head.

The group was back in Atlantis forty minutes later, and John sent a message to Major Lorne to get a team together for the extraction. Elizabeth gasped when she saw the blood seeping through the hastily applied field bandage on his arm, and added her own command to Carson's that the debriefing take place in the medical room.

With her arms crossed, Elizabeth listened to the story of what had happened with Ellia and the stolen test serum. A worried frown remained in place on her face the whole time. While the others took turns with parts of the tale, Carson cleaned and bandaged the cut on the back of Teyla's head before turning his attention once more on John. Rodney and Ronon asked to be excused when their parts in the story had been related, both heading off for a shower, change of clothes and, no doubt, a large meal. John smirked at the thought of the similarities between the otherwise disparate men.

John gritted his teeth when Carson swabbed the wound in his forearm carefully for a DNA sample and scraped a small section of flesh from the area for the same reason. When he had handed them off to a nurse, Carson applied antibiotic cream and bandaged the area.

"Until Major Lorne and the others get back with the body and I run tests on these samples," Carson told Elizabeth, "I won't know the full ramifications of her attack on the Colonel. Teyla needs to stay the night for observation in case of a concussion, and Colonel Sheppard should probably stay as well, just in case."

"Alright," Elizabeth nodded.

"Hold on a minute," John said. "I feel fine. She didn't feed on me." He gestured to his head, "See? No grays."

Carson shook his head, "By the time she attacked you, I don't think Ellia was truly a Wraith any longer. We have no idea what kind of reaction you'll have from the wound, son."

"Look," John made himself say sternly. He really didn't want to stay in medical any longer than he had to. "I'm fine. You said yourself that she was more of an Iratus bug than anything else when she cut me. Once the first bug was off me and you restarted my heart, I didn't suffer any unusual side effects."

Carson didn't have a rebuttal to that, but the worried frown on his face didn't lighten any. Usually that wasn't such a big deal since Carson was always anxious whenever any of the people under his care were sick or injured, but his frown was causing deeper than normal furrows in his forehead. John realized the good doctor was feeling guilty.

"Beckett, you couldn't have known Ellia would do what she did. You were just trying to help."

"John's right, Carson," Elizabeth added. "No one blames you for how this turned out. From what you've all said, Ellia was a very desperate young woman. Now, John, I realize you feel fine now, but I want you to promise me you'll report back to Carson the second you feel at all badly, even if it's just a headache."

In the face of Elizabeth's still very worried expression and Carson's quiet watchfulness, John sighed, "Fine. The second anything bothers me, I'll report back. Can I go now?"

Elizabeth had to stifle a smile at the pleading-little-boy expression he adopted as he had known she would and, after a confirming glance at Carson, she nodded.

It was on the walk to his quarters that John had a horrible thought. When he had been insisting he was fine, he had almost insisted that he felt better than okay, the very same thing Ford had said when he had been injected with an overdose of the Wraith enzyme. Right before he had gone crazy from his addiction to it. Feeling another twinge in his arm, John shook his head at his own thoughts. The wound hurt and he didn't feel like super-anything, so it must just be his conscience hassling him for not being able to spend more time looking for his friend.

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The next day Carson pronounced Teyla clear to leave the medical room. She was sent by the doctor to find John and ask him to check in at some point during the day. John was on his morning run with Ronon when she found him, the taller man a good twenty feet ahead of the Colonel. John jogged to a stop in front of her and smiled.

"Head feelin' better?" he asked.

"Very much, thank you for inquiring," Teyla answered as politely as ever. "Colonel Sheppard, Doctor Beckett would like you to go and see him when you have a free moment."

"Thanks, Teyla." He glanced in the direction Ronon had gone, and shook his head, "If you see Ronon, let him know I cut my run short this morning, will ya?"

Teyla nodded, and John headed in the direction of his room at a brisk walk. Once there, he stripped out of his sweaty clothes and headed for the shower in his in-suite bathroom. Turning the stream of water on to the temperature he liked, John leaned against the sink momentarily to gently peel off the medical tape holding the bandage to his forearm. He tossed it into the garbage before climbing into the shower.

He stood still for long minutes with his head tilted forward, letting the hot water pound on his upper back and shoulders, easing tension and tight muscles that had more to do with stress and worry than anything physical. When John stepped out ten minutes later, he quickly dried himself with a large towel. He hissed in pain when he unthinkingly rubbed his right arm vigorously. Dropping the towel, he stared at the wound on his arm. There were several small lines of blue creating a web-like design expanding from the site.

"Damn it," he swore fiercely.

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Elizabeth entered Carson's office off the infirmary to find Rodney, Teyla and Ronon already there. She took the fourth chair that had been placed in front of Carson's desk, her stomach in knots. The Scot wouldn't have called them all in with John sitting in the infirmary a room away if it was good news. Good news would have been handed directly to John, reported to her and that would be the end of it.

"I'm afraid I have some bad news," Carson unknowingly confirmed Elizabeth's thoughts. "Colonel Sheppard has been infected by a mutated strand of the retrovirus through the wound on his forearm."

Rodney was pale as he rebutted, "Then why isn't he a snarling monster bent on destruction? Ellia was transformed in a matter of minutes."

"Aye, but Ellia, being a Wraith, already had Iratus bug genetics; the Colonel didn't. The tests on the samples I took when we first got back from the planet show a small amount of what the retrovirus became after it had altered Ellia. The Colonel came to me half an hour ago to report that the area around the wound has changed color and texture, the first sign of what I fear will be a transformation much like Ellia's. I've taken more samples, and I suspect they'll show a higher concentration of the retrovirus in the Colonel's blood and tissue."

"You're working on a cure, right?" Elizabeth asked.

Carson flinched. "Aye, lass. I've already got all of my team working on it. I'm afraid I won't know much more until the second round of tests come back."

Ronon's chair suddenly and forcefully scraped backwards making the others cringe at the sound, and the dark man stalked from the room with long strides.

"What was that about?" Rodney asked.

"I believe Ronon is feeling guilty," Teyla answered softly. "Colonel Sheppard ordered Ronon to stay with me when I was injured, and Ronon obeyed the order until I awoke and told him he sometimes must choose to go against orders when he knows they are wrong. Ronon believes if he had been with the Colonel, Ellia would not have been able to attempt to feed on him."