Dark Conversion Chapter 3, a stargate: atlantis fanfic

Author's Note: Italics signify thoughts or emphasis. Part 3 of 5.

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When Elizabeth led him to the lab where months ago they had found her ten thousand year old self, John was relieved and worried at the same time. It would be great if putting him in stasis gave Carson enough time to come up with a treatment or cure, but part of him was terrified of not being aware. What if something happened to the city, to Elizabeth, to everyone? They could be destroyed by the Wraith as he slept and he'd never know it. Would he wake ten thousand years from now to find everything he had ever known gone? But when he glanced at Elizabeth and saw the hope burning in her expressive eyes, he knew he had to let them try it.

Rodney was already in the room, his laptop hooked into the machine's interface. He smiled distractedly at them when they entered the room, gesturing John toward the chamber they'd found the aged Elizabeth Weir in. John pulled off his cloak before getting in, knowing from having fallen asleep with it on once that it wasn't the most comfortable thing to be unconscious in. Rodney gasped but John ignored the sound, knowing it was only shock since Rodney had not seen him quite as… Wraith-buggy… as he was now.

As he climbed into the device and lay back against the smooth, slanted surface, John was disconcerted and yet somehow comforted to find that it still bore Elizabeth's scent. The fact that he could even tell that didn't bother him as much as he thought it would. Heightened senses… it kind of made him feel a bit like the superheroes he had pretended to be while playing as a child.

"We're just going to do a test run first," Rodney commented. "If it works, we'll wake you up and let Carson get some last minute samples and such and let you take care of anything you need to before we put you under more long term."

John nodded his understanding and Rodney turned back to his computer. Elizabeth gave John an encouraging smile that he returned before closing his eyes. Knowing there would soon be a barrier mere inches from his face, John was suddenly glad that he had never been claustrophobic. He sighed softly, wondering if he'd feel anything when the machine activated.

Rodney swore colorfully and started madly tapping on the keys of his laptop. John's eyes flew open and settled on Elizabeth. She was watching Rodney worriedly. Realizing that something wasn't going as planned, John got out of the chamber and approached them, making sure to stay closer to Elizabeth since she wasn't as jumpy about his changed appearance.

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Rodney hung his head in defeat and Elizabeth voiced what they all realized, "It didn't work."

"Of course it didn't work," John scoffed. "Rodney thought of it. I'm surprised it didn't explode and kill us all."

Rodney flinched visibly, and Elizabeth frowned at the infected man, reprimanding, "John!"

He looked at her, his eyebrows raised over his oddly different eyes. It was his 'everyone's thinking it, so I said it' look, but she had never heard him be so deliberately cruel before using it before. At least not to his friends. Elizabeth couldn't think of a way to respond, and John turned and left the lab.

"He's not himself, Rodney," she said when she found her voice.

Rodney shrugged and continued staring at the screen of the laptop attached to the cryogenic chamber's controls, trying to hide how deeply John's comment had cut. Ever since the disaster on Durandan he had been trying to re-prove himself worthy of everyone's faith and trust, John's especially, and he had just failed again. But Elizabeth found it impossible to try to comfort Rodney further when she was still so worried about the bigger problem of John's health. She couldn't help feeling that she, too, was failing the man who had gone to so many extremes so many times to protect her and the other members of the Atlantis expedition.

And she had absolutely no idea what to do about it.

"As far as I can determine," Rodney informed her quietly, "the sensors refused to recognize the Colonel as a human. The Ancients must have built in a failsafe so that the Wraith could never use it. It makes me wonder how different the Wraith hibernation chamber technology is from this."

Elizabeth perked up. "What about that crashed ship you explored a few months ago, the one where you encountered the solitary Wraith? Did it have hibernation chambers? Maybe you could reverse engineer one that would work for him."

"It was just a transport ship, not a full hive ship," Rodney replied despondently. "If it'd had chambers the crew wouldn't have turned on each other for sustenance."

Elizabeth closed her eyes and slowly shook her head. They had come up with only one solution to John's problem, however temporary, and it hadn't worked. She couldn't help but wonder if John now regretted ever choosing to come to Atlantis.

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That evening, Elizabeth was working in her office when someone clearing their throat alerted her to the fact that she had company. She looked up, surprised to see Ronon Dex filling her doorway. He always treated her with respect, probably because John did, but Ronon had never actively sought her out for anything before.

"Can I help you with something, Ronon?" she asked as she waved him into the room.

Teyla entered the room as well. The petite Athosian had been hidden behind the much taller man a moment before.

"Teyla?" Elizabeth added to her question.

"I need to go off world," the man who had rarely said more than one word at a time to her replied.

Teyla huffed softly at his bluntness and attempted to elaborate for him, "Ronon and I went to see Colonel Sheppard earlier. He was quite rude to us, and Ronon took offence. He and Colonel Sheppard almost came to blows."

Elizabeth sighed and leaned back heavily in her chair. She knew from the latest mission report that Ronon was blindly hateful of the Wraith, not that she could blame him with what he had been through. But the current situation must be difficult for him to deal with. Everyone had seen the respect and loyalty he gave John, and now John was turning, more or less, into a Wraith.

"And you're afraid if you are confronted with each other again while he is in this condition that one of you may end up hurting the other?"

Ronon nodded once to show that Elizabeth had guessed correctly. "I also have something to take care of."

"To show that he has every intention of coming back and keeping his word to keep the city of the Ancestors a secret, Ronon has asked that I join him if you allow him to leave Atlantis," Teyla informed her. "And I have agreed."

"Very well," Elizabeth conceded. "But be careful."

"Thank you, Dr. Weir," Teyla responded.

Ronon added an appreciative grunt to the end of their conversation.

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Three days later, the alarm sounded for an unscheduled incoming wormhole.

"Shield up," Elizabeth told the man at the control panel.

She waited tiredly, knowing she didn't have the energy or the heart to deal with another crisis on top of the one that was now getting worse by the hour instead of by the day. Morale was at an all-time low with the military leader of the city not expected to recover and the flagship team no longer together. Elizabeth could only be thankful that Colonel Caldwell was safely out of the way in the Milky Way galaxy picking up more supplies and personnel. If she had to deal with him on top of everything else and he made one of his usual snide remarks about John, she would have gladly shot him right between his smug, squinty little eyes. And not with a stunner.

"It's Teyla's IDC, ma'am," the man at the 'gate controls reported.

"Open it."

With a flash, the shield disintegrated from the surface of the event horizon. Moments later Ronon stepped through, a body slung over one broad shoulder. Teyla followed, keeping a Wraith stun weapon trained on the figure being carried by her companion. Ronon turned to say something to Teyla, and Elizabeth got a better view of his captive from her balcony. It was the long-missing Lieutenant Aidan Ford.

Her eyes wide, Elizabeth ordered the nearest military officer to get a team down to the 'gate room immediately. She left the balcony and control room area quickly to move down to the 'gate room herself.

"What…" she trailed off, unsure what exactly she'd meant to ask.

"I made a promise to Sheppard to get his friend back for him," Ronon said gruffly. "I keep my promises."

He didn't add 'before it was too late' but they both knew that was a large part of why he'd found it necessary to go looking for Ford now when he hadn't in the weeks since joining up with them.

"How did you find him?" Elizabeth asked.

"Wasn't hard since we weren't recognizable to his scouts as being from Atlantis," Ronon replied. "He was recruiting those hit hardest by the Wraith to join in his fight against them. Promising to help make them as strong as he is."

"Perhaps it would be best to continue this conversation once Lieutenant Ford is safely secured," Teyla remarked.

Though the Athosian still had the stun weapon trained steadily on the young man she had considered her friend, Elizabeth could now see in the other woman's eyes how nervous she was. There must have been quite a fight between Ronon and Ford. Elizabeth nodded in response to Teyla's comment and led the way to the holding cell that had been home so far to two Wraith. It felt wrong to put one of their own in it after it had been occupied by 'Steve' and 'Bob,' but Elizabeth had to acknowledge it was probably the only way they could hold him until Carson could find a way to free Ford of his addiction to the Wraith enzyme.

Ronon set his burden on the floor of the cell and stepped back beside Elizabeth. The energy shielding around the cell was activated. Elizabeth ordered a full guard detail on Ford, with her being their first notification when he woke. She left to head for John's room, hoping the news would raise his spirits a bit.

When she reached it, however, the guard positioned outside his room told her he was sleeping. Disappointed that she couldn't cheer him up with the news yet, Elizabeth went to her office to work on some of the paperwork she had fallen so behind on the last several days. Less than an hour later her earpiece crackled to life, a frantic voice telling her that Lieutenant Ford had escaped when Dr. Beckett, believing Ford to still be unconscious, had entered the cell to take a blood sample. Dr. Beckett was being treated for a broken arm and one of the guards for contusions and a possible concussion.

Right after that, the guard from John's room contacted her to let her know that the Colonel had left his room in the direction of the 'gate room at a dead run. His guard had been unable to keep up but he was on his way.

Elizabeth got out from behind her desk and exited into the control room, only to find Grodin's replacement and the rest of the staff slowly backing out of the room, a crazed-looking Ford waving a gun at them. John entered the doorway on the far side of the room a moment after everyone else was gone. Ford stilled and simply stared at the changes in his former CO.

Even Elizabeth was surprised at the severity of John's condition. He had been avoiding contact with her the past couple days since the failed attempt at putting him in stasis, but she hadn't fully realized what the passing time meant to his status. Or maybe she just hadn't wanted to. The blue, mottled skin had spread, what she could see of his arms no longer held any hint of human flesh tone, and the color on his neck had spread to also cover most of the lower half of his face. There were hints of the color on his forehead and the area around his yellow-green eyes. The spines and ridges on his arms were more pronounced and there was evidence of more of them growing in on his jaw line.

"What the hell happened to Sheppard?" Ford yelled when he got over his shock. His gaze spun in an arc around the room, landing on Elizabeth. "You let this happen to him."

He stalked toward her, the weapon he had undoubtedly stolen from one of the guards pointed directly at her head. Elizabeth was frozen, knowing from what the others had told her and what she had observed of his behavior that Ford was not going to listen to reason. In fact, she might very well make it worse if she didn't keep her mouth shut.

Elizabeth was unable to prevent the gasp from escaping her mouth when the blurred form of her mutating second-in-command moved between she and Ford. "John!"

Surprised by the lightning fast move, Ford's hand jerked, pulling the trigger of his stolen gun. The bullet struck John's shoulder and Elizabeth let out a small shriek, but John barely flinched. He reached behind him with the same arm, and when his hand motioned her to come closer, she obeyed, keeping herself nearly pressed against his back as he warily edged around Ford. Elizabeth wasn't sure if he was trying to find the best route of escape or the best way to attack Ford. The only thing she knew for sure was that she trusted the mutating man with her life much more than the younger one who was now clearly off his rocker. Actually, the same most likely would have been true even if Ford had been completely normal.

"Mine," John growled warningly to Ford when the younger man tried to train his gun once more on Elizabeth.

Ford looked surprised for only a moment before the frown on his face deepened, "Get out of the way, Sheppard. I don't want to go through you to get to her, but I will if I have to."

Elizabeth stumbled when her hip struck the corner of a desk, and Ford made his move. He darted to the side so that John was no longer between Ford's gun and his target. Fortunately, John was faster. Elizabeth watched in a mixture of horror and relief as John snapped Ford's neck before the enzyme-addicted young man even knew what hit him.

John was breathing hard as Ford's body slipped to the floor. Major Lorne appeared at the doorway, taking in the situation with a quick glance.

"Shut down the alarm," he said over the comm in his ear. "And call off the search, Lieutenant Ford has been found and neutralized."

Elizabeth was still watching John, who was switching his gaze between her and the man in the doorway. He was still wary, holding his body tensely.

Lorne took a step toward Elizabeth, asking, "Are you alright, ma'am?"

With a feral snarl, John leapt across the room, once more putting Elizabeth behind him. Major Lorne raised his weapon quickly, training it on John's chest. Elizabeth roused herself from her shock enough to find her voice.

"Stand down, Major," she ordered as calmly as she could. "Back away slowly."

Lorne frowned but followed orders, lowering his weapon... though Elizabeth could tell from his stance that it would be raised and used in a matter of seconds if he thought it necessary to protect her. After an obvious hesitation, he backed toward the doorway he had come through. John reacted, straightening from the slight crouch he had been in and reaching out to touch her, as if to reassure himself that she was there.

"I'm okay," she told both men. To Lorne she said, "I think it would be best if I led the Colonel back to his room. He's much more likely to remain calm that way."

"Yes, ma'am," Lorne responded, ordering the other guards out in the hallway to stand down and clear the way.

Elizabeth gently grasped John's hand, hoping she was right and that he would let her lead him back to his room. Though he kept his eyes on Major Lorne, John did allow her to guide him. It was a slow process, Major Lorne walking backwards about fifteen feet in front of them, clearing hallways as they went so no one would cause a reaction in the still agitated Colonel. When they reached his room and Elizabeth opened his door using the control panel beside it, John tugged her forward into the room with him.

Major Lorne raised his weapon again, but Elizabeth said, "It's alright. He just wants to know I'm safe. When he calms down, I'll come out."

"Ma'am…" Lorne tried.

"Major, if I need you, you'll know it, trust me."

"Yes, ma'am," he agreed reluctantly as he watched the door slowly slide shut between them.