Disclaimer: Stargate Atlantis and its characters belong to their appropriate proprietors, creators and owners. No copyright infringement is intended. This story was created for entertainment purposes only. No profit has been made from this. Only original characters and storyline belong to the author.

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Title: Uncommon Alliance
by Stargalaxy

Chapter 32

Elizabeth frowned, her features hard as she shook her head. "No, John. I'm sorry but I can't allow you to do this."

She still found it difficult to get over the fact that Sheppard had somehow overheard their conversation. When she questioned Ronon about it, the Satedan had informed her that he hadn't heard anything and all knew that the Satedan has sharp hearing. It looked like the change in the colonel's DNA was definitely giving him sharper senses. If she had known, she would have taken steps to prevent him from knowing about the IOA's threats to her position. She knew that it was one reason why he was agreeing to do this for John would always do anything to protect his team and those in Atlantis even if it was to his own detriment.

"Do you know what you're going to allow yourself to be put through, John?" she asked him evenly, her gaze locked onto his.

Hazel-green eyes stared back at her. "I have a fair idea," Sheppard replied stubbornly. "But I can't allow you to l-lose your job because of me. Besides, there's n-no other option. I have to…" he paused to catch his breath, "…handle this myself."

Beckett frowned. "You're getting weaker, lad. Our Wraith prisoner is dying, I'm afraid that there's only so much I know about Wraith physiology. While we're doing everything we can to try to keep it alive his outlook doesn't look promising."

"Are you sure there's nothing you can do to save it?" Weir asked the doctor.

"Not unless we are willing to sacrifice a human being for it to feed on, Elizabeth."

"But it killed and fed on Lt Cumins when it escaped. I saw the lieutenant's corpse myself or at least what was left of it. Wouldn't that have been enough for it self-heal?" Caldwell asked.

Beckett shook his head. "No, the Wraith was already starving. When it consumed the lieutenant's life-force, it might have eased its hunger but it wasn't enough to regenerate all its cells when Sergeant Tucker riddled it with bullets. The fact that it had recently fed upon Lt Cumins is probably the reason why the poor bugger isn't dead yet. It managed to heal some of the damage done but not all."

Teyla spoke up. "I believe that it does not wish to live."

Sheppard gave her a sharp look. "Why n-not?"

The Athosian shook her head and eyed Sheppard sadly. Her arm was still in a cast but Carson had already discharged her from the infirmary. "Dr Beckett asked me to try to link with the wounded Wraith in an attempt to find a way to save it. When I did so, I sensed only deep anger and hatred emanating from it. It burns with bitterness and hostility, desiring only our destruction and that of Atlantis. However, as it knows that that is something that it cannot have at present, it seeks its own death. In death, it knows then that we would be unable to extract anymore information from it."

"Aye, I agree with Teyla's assessment," Beckett added.

When Sheppard asked how they had managed to capture the Wraith, they told him about it.

Weir appeared troubled. "Are you sure you're up to confronting the IOA representative, John?" she asked again. "You do know that I'm willing to fight them on this."

Sheppard didn't answer immediately but studied his team. All of them were staring at him intensely. He knew that they didn't want him to do this. In fact, Ronon was scowling darkly at him, his arms crossed over his chest, shaking his head slightly clearly implying for him not to do this; Teyla was obviously unhappy and disapproved of it too; and McKay huffed in annoyance, saying, "Dammit! Sheppard, this is ridicules! We'll find a way to hide you, smuggle you away, at least until you're better. But for freakin' sake, do you honestly want to be put through the wringer by the IOA?!"

"My people would accept you into their homes anytime, John." Teyla offered, clearly hoping that he would take up the offer. "You have done much for us. Please let us do this for you."

However, Sheppard pursed his lips and shook his head. This was something that he could not run away and hide from. It had to be dealt with sooner or later and personally he preferred sooner. He was always one to grab the bull by its horns, act on his emotions, as he was not one for procrastination.

"No, if I did t-that, it would imply t-that I'm guilty. Let me t-try to reason with the guy first. If things take a turn for the worse, then you can do w-what you want."

Weir folded her arms together and nodded; her gaze intense with concern. "Very well John. However, if you still want to do this, you should know all the facts, I'm afraid that I have more bad news for you. I've received recent instructions from the IOA again. It seems that they heard about what happened in the infirmary. They're afraid of you getting violent again. Therefore the IOA has ordered that you to be handcuffed when their representative arrives to question you."

Sheppard froze at that. This was something that he hadn't expected, to be treated like a criminal even before he had a chance to defend himself. He felt his muscles becoming tense, his heart rate accelerating slightly, his tension headache increasing. He forced himself to remain calm, to take slow deep breaths. He knew that he had hurt some Atlantis personnel when he had lost it yesterday. Although no one had been seriously injured, many were sporting bruises and black eyes.

"John? You okay?" Elizabeth asked him, and he felt her hand gently gripping his shoulder, checking whether he was all right.

He took a swallow and eased his breathing, looking at Snacks sleeping on his lap. "Yeah, I'm okay."

However, McKay came striding forward, obviously unable to contain his frustration over the entire situation. He came to John's defence when he saw that Sheppard wasn't going to argue the point. "I don't freakin' believe this! The IOA deserves to be shot! That's a load of crap!" McKay rounded at her. "Now you know that wasn't Sheppard's fault! God, everyone has a breaking point, waking up, getting attacked by a Wraith, I would say that constituted a damn good excuse for his delirious behaviour!"

"I concur, Rodney has a point," Carson added.

Weir nodded. "Yes, I know, none of us are blaming John over what's happened. Even Heightmeyer wrote a report out for John in his defence stating that it was probably the result of PTSD. But the IOA are taking no chances and they are refusing to reason with us on this matter."

She sighed. "Look, John, you don't have to do this, I could try…"

"No, Elizabeth," he cut her off before she could complete her sentence. He felt touched by their desire to protect him. But this wasn't their battle to fight. "I will c-comply with the IOA's wishes…." He paused, frowning at his stutter. "Dammit, Carson! W-why am I still s-stammering?!" he shot a frustrated look at Beckett.

Carson shook his head sympathetically and said, "Just a reaction from the Wraith implant, lad. Our tests showed that your synaptic nerves are still trying to deal with the trauma of the Wraith implant. Just give it time to heal lad, your stutter should go away in time."

"I h-hope so doc," he replied, his insides still churning over what he had just agreed upon. But he knew that he was right, that he had to do this. That he had to face the IOA, that there was no other choice. Realistically, he knew that he wouldn't be allowed to remain in Atlantis if the IOA or SGC suspected that he had been compromised. He would probably be shipped back to Earth to rot in some military prison.

However McKay wasn't willing to give up the fight. His hand was gripping his neck, indicating that the scientist still suffered from a sore neck. "Have you completely lost your mind, Sheppard?! You are not a prisoner or a criminal here but a victim of whatever hell that Wraith put you through! You don't have to agree with this! You don't have to take this sitting down! Especially not from the IOA!"

He knew that McKay meant well but he was getting fed up of having to explain himself to everyone. "Believe me, Rodney, I am not t-taking this sitting down! But if the IOA wants to q-question me, it's within their r-rights to do so. It is n-not something that I want to do but what I have to do! I have f-fight my own battles, McKay. No one else c-can fight it for me. If I don't do this, I w-won't be allowed to stay in Atlantis a-and definitely not as her military commander!"

McKay looked shocked at his outburst but the message finally sunk in.

"Colonel Sheppard's correct," Caldwell interjected while he folded his arms across his chest. "The military does not look kindly at the prospect of potential traitors in their ranks. No offence, colonel."

"None t-taken, sir," the pilot replied wryly.

Caldwell nodded as he continued. "I see this as Sheppard's best course of action. If he wants to continue to stay on Atlantis, he has to agree to this."

"Thank you, sir," said Sheppard, glad that someone understood where he was coming from, even though it turned out to be Caldwell. But then both of them were military men serving the US Air Force, they understood how things worked. He coughed softly, still feeling slightly shaky and feverish, but that couldn't be helped. He wondered whether he could ask Beckett to provide him with some stimulant that would boost his strength to allow him to get through the interrogation without collapsing.

"Carson, can I c-change into my uniform? I'd prefer not t-to be in scrubs when I meet the IOA representative."

Beckett understood. "Aye, lad. I'll see that someone fetches your uniform for ye."

Caldwell cleared his throat and he looked a little uncomfortable as he spoke up again. "Colonel Sheppard, I believe that you should know that the IOA also instructed us that you're to be placed in an isolated ward during the questioning."

Beckett nodded and sighed. "Aye, lad. If you agree to this, we'll be setting up the observation room where we originally kept Michael."

So, the IOA is really going to treat me like a criminal, Sheppard thought bitterly to himself. "I understand," he replied, "Do what w-what's required." At least he would be allowed back into his uniform again, so that should count for something.

"I'll drop by your quarters, colonel and get your clothes," McKay offered.

"Thanks, Rodney," he murmured. Absently, he petted the little Talmera that was still snoozing on his lap.

Before they left, Sheppard turned towards Weir, McKay, Teyla and Ronon. "Can I speak to you guys privately for a moment? Not necessary now, but sometime soon." He knew that he had to tell them about Lf'wyne. If they couldn't find a cure for him, he would have to leave Atlantis soon.

"Of course John," Elizabeth replied. She looked at the time and frowned. "We don't have much time now, Mr Rogunie would be arriving soon. I'll see you after you've met the IOA representative?"

Sheppard nodded. "Sure, afterwards is f-fine."

---

As Weir and Caldwell exited the infirmary, Caldwell stated solemnly. "I must admit that I'm a little surprised, I never expected Colonel Sheppard to agree with this."

Elizabeth turned to study the Daedalus commander walking beside her. When she spoke, her gaze and voice were frosty. "That is why John Sheppard doesn't deserve this treatment, Colonel. That is the same man whom you had placed in restraints in the stasis pod; the same man whom you claimed - not so long ago I might add - might be compromised by the Wraith."

Caldwell thought about her words and the man whom he had just left. He felt ashamed and a little guilty that he had doubted Sheppard's honour and loyalty to Atlantis and her people. The fact that he was willing to go through the trial and humiliation to proof his innocence impressed him greatly.

"It looks like I might have been mistaken," he added softly.

Weir was surprised. It wasn't often that Caldwell admitted to a mistake.

---

Sheppard was standing in the isolated ward dressed in his standard BDUs again. There was an empty table in the middle of the room and two empty chairs, one was for him and one reserved for the IOA representative. Beckett and McKay had just left the room, leaving him alone now.

Before they had left, Beckett had looked at him and said, "You sure you want to do this, lad?"

"Not want to, Carson, b-but have to," he repeated again. Earlier the doctor had found a stimulant that his body didn't react badly to. Although the Scotsman had been reluctant to administer it to him, Beckett saw that the need was pressing and had done so unwillingly. As a result, Sheppard felt stronger now, more capable of facing what was in store for him.

"Aye, sorry lad, I understand. I just wish there was something more that we could do."

"That's okay doc, t-thanks for your help."

Beckett left leaving McKay in the room carrying Snacks in his arms. "Well, good luck Sheppard. I still think you're nuts for doing this. But don't worry about Snacks, I'll take care of it while you're being put through the wringer."

"Thanks Rodney," Sheppard replied wryly as he reached out to scratch the little Talmera under the neck. Snacks squeaked in delight at him and gave him a little tail wag and a one sided wing flap.

"Oh, did you see that?!" McKay asked a little excitedly. "I'll say that our little friend is getting eager to fly again."

"I won't be surprised," Sheppard said, giving it a final pet and feeding it a small piece of powerbar that he held ready. Snacks gobbled it up in two bits and licked its lips. The pilot smiled before he looked up at Rodney again. "I'll see you both l-later."

McKay nodded as he headed out the door. "Good luck, Sheppard. Give the IOA guy hell."

A little while later, Major Lorne arrived carrying a set of handcuffs with him. Sheppard tensed immediately as he held out both hands in front of him. The young Major looked clearly unhappy about this.

"I'm sorry about this, Colonel," he stated apologetically. He looked at Sheppard then as if asking his permission for what he was about to do.

"Not your fault, Major, just do your duty." He was pleased to note that his voice sounded calm enough, displaying no evidence of his frazzled and tensed nerves.

"Thank you, sir," Lorne replied, as he attached the security hand cuffs on his wrists.

Feeling the cold edge of steel encasing his wrists instantly evoked unwanted memories of his torture and experiments by the Wraith. He clenched his jaw tightly and swallowed hard, fighting to control the raw emotions that he felt rising deep within him at the memory. He felt his heart beat accelerate and cold sweat break from his skin. His gut also twisted with painful tension from the stress he was feeling at the moment. Sudden nausea threatened to overwhelm him.

"Sir… Are you all right?" Something must have shown on his face, betraying his inner feelings, for he saw the young major looking at him with open concern now.

He swallowed again and nodded. "Yes, I'm fine," he replied as he forced himself to remain calm and hold down the nausea. He had lost it once in the infirmary; he refused to lose control again. You're a soldier dammit! Get in control of yourself. Now is NOT the time to lose it! he silently reprimanded himself.

He looked down at the shackles in his hands again trying to be grateful that Lorne had the decency to place them in front of him instead of behind his back. The fact that the handcuffs were reasonably large that they didn't chafe his wrists badly was also a bonus. It also meant that he had still some limited maneuverability in his hands, which was a good thing. Lorne gently helped him to sit on the empty chair beside the square table as if he suspected that Sheppard was still trying to recover from his state of shock. Sheppard knew that the major would have felt the slight tremors of his body, but if Lorne noticed it, he made no sign of it, to which Sheppard was eternally grateful.

When Lorne and his security team left, he sighed, wiping a thin layer of sweat from his face. He looked up at the glass observation deck above him. He knew that there was where his team, Elizabeth, Carson and Caldwell would be observing him during the questioning session. If it was one thing that he hated was the feeling of being watched like some lab mice. He shook his head and sighed, forcing himself to calm down.

You can do this, John. You can do this, he told himself over and over again. He had survived being interrogated by Daffy the Wraith. Surely he could deal with one lone IOA agent.

---

At exactly three pm sharp, Mr Rogunie stepped into the room, punctual to the second. He was a well-dressed man in a pinstripe suit, his blond hair and beard neatly combed, not a single strand of hair out of place.

"John Sheppard, I presume?" Rogunie had a cool voice and a collected manner. The tall burly man hadn't addressed the pilot by his rank; Sheppard knew that there had a reason for it, and he didn't like its implications.

Sheppard saw the man's eyes roam, taking in his uniform and his unruly dark hair. There was a slightest look of scorn hinted in his cold blue eyes and a tinge of a smile formed when his sharp gaze took in the metal shackles on Sheppard's wrists.

"Yes," Sheppard curtly replied.

"Good," he stated, "I am Mr Rogunie, Karl Rogunie. I'm sure Dr Weir would have briefed you about why I'm here." He extended a hand out to him.

He looked at offered hand but made no move to shake it. After all, he was in handcuffs, and this man had done nothing to earn his respect. "Yes, I k-know who you are," Sheppard finally stated. He frowned, hating his stutter. He saw the IOA representative's lip curl up slightly in a sneer.

"Good," Rogunie sat himself down on the empty chair. He scrutinised Sheppard for a long moment before he started to speak. "Sheppard, I'm here to inform you that you are relieved of duty as military commander of Atlantis. Colonel Caldwell will be taking over your role until further advisement." His attitude was too calm and collected; his voice was monotonous, with no variation or emotion in it. Sheppard suspected that the IOA representative was purposely not using his rank because he wasn't about to give him any rights.

"Oh, joy," Sheppard quipped sarcastically. He saw a shadow of an annoyed frown crease the other man's forehead before it quickly disappeared. He had already expected this, it was nothing new, but that didn't mean that it didn't leave a bitter taste in his mouth. So, it begins, he thought darkly to himself. Anger bubbled deep within him but he used it give him strength instead. He knew that once Rogunie got over the introductions and niceties, the interrogation would begin.

To be continued

---

Note: Regarding the captured wraith in Atlantis, this wraith does not belong to Lf'wyne's hive. It's more associated to Daffy's hive. Hopefully, that clears things up a little. Sorry to those who might be upset that it's dying as it needs to follow the planned plot.