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.

Title: Uncommon Alliance
by Stargalaxy

Chapter 27

He came to the world sluggishly. He felt cold, freezing cold and sick. His mind felt fuzzy with a pounding headache as if he was suffering from a long, drawn out fever. Opening his eyes, he saw someone bending over him, looking at him from an opening above. He seemed to be in some sort of containment chamber. Where am I? Why am I so cold? His teeth chattered, his breaths were coming out in white puffs of smoke. There was the smell of frost in the air…

"John…, John? Can you hear me?" he heard a female voice call his name as a hand reached out to squeeze one of his cold clammy hands that was positioned on top of him. There was something freezing cold, almost burning, attached to his wrists; he wondered about them but felt too weak to turn his head to look or to lift his arms.

"You're going to be all right, do you hear me, John? You're home now and you'll going to be all right." He thought he recognised the voice. It took him a while to realise that it was Elizabeth speaking to him.

"H'me...? El'b'th?" he muttered weakly, surprised to find how weak his voice sounded. Yet, he was wary, uncertain whether to believe her. The memory of a dream arose suddenly, of him walking in a wheat field… of someone – a friend - waiting for him there…

"Yes, John, it's Elizabeth, you're save now, you're home," her voice seemed to smile. "We're going to help you, John."

It was quite difficult to concentrate on Weir's words from amidst the cold he felt and the pounding of his headache. At the same time, he tried to brush away the memory of the wheat field and focus on the words that were being spoken to him. He saw another figure approach him beside the blurred image of Elizabeth.

"Hey, buddy, just hang in there…" Again, it took a little while for his mind to register the identity of the person speaking. Rodney? There was a moment of irrational fear at seeing Rodney, which he pushed down with a force of will. No, this is the real deal, this is real! He's not a doppelganger! The dream of the wheat-field came back again and he remembered Lf'wyne telling him that he was back with his people again. He blinked trying clear his blurred vision. He hoped to God that this was real.

"You really had us worred there, Sheppard, thinking that the Wraith might have made a main course out of you."

"Rodney!" Weir's shocked voice rebuked the scientist for his bluntness.

"What? It's true isn't it?" McKay replied.

It certainly sounded like McKay. Am I really home? Hope and excitement stirred within him. He stared at the blurred form of Rodney. He recalled running into his team on the Wraith planet, fighting them, thinking that they were doppelgangers. He also recalled waking up somewhere else, of Carson being there, assuring him that he was onboard the Daedalus, that his team was the real…

"N't dre'm?" he asked sluggishly.

Another head came into his view; this time he recognised the pointed dark hair and the Scottish brogue instantly. "Aye, lad. We're real, it's not a dream. We're going to take care of you, lad. Just hang in there."

"You had us all pretty worried, you know. But it's good to have you back," Elizabeth said gently. Despite his blurred vision, he knew that she was smiling down at him.

Sheppard swallowed, pursing his lips, feeling an emotional lump form deep inside him. His body started to tremble and he felt ashamed that he had no control over it. He wasn't sure whether it was because of the cold or from unshed tears of relief. Suddenly, he no longer cared how screwed up he appeared. He was home, after all this time he was finally home; no more interrogations, no more experiments, no more false-evil teams whose only purpose was to hurt him and get him to betray his people. If there were no witnesses about, he might have broken down and sobbed there and then. The relief he felt was overwhelming. Instead he squeezed his eyes shut, halting the tears as he released a gasp filled with unexpressed emotion.

"Colonel, are you all right?" he heard Beckett ask him in concern.

"Of course, he's not all right! Look at him, he's a mess! Now stop asking him silly questions and fix him up!" The voice of McKay interjected above him.

A small smile creased his lips. In all his hallucinations, McKay's sarcastic wit was always off. This time, it sounded real enough to convince him that perhaps this time it was truly real.

He felt the edge of his vision darken and the roaring sound in his ears got louder. He was dizzy, the pounding in his head felt as if it was killing him; he knew that he was falling unconscious again despite the unnatural feeling of strength surging through his body. It felt too familiar… as if the strength attributed to a Wraith's presence… He frowned, trying to analyse it. No, it can't be. He told himself. Atlantis doesn't have any Wraith here, it must be something else… Beckett… Carson must have found a way to help me…

As if from far away, he heard another voice speak, a male's voice… Caldwell…

"Drs Weir, McKay, I must advise you to please move away from Sheppard… He might be dangerous…"

Sheppard frowned. What the voice said didn't make any sense. I must be dreaming…

"Caldwell, you're kidding right?" McKay stated above him in a tone dripping with disbelief. "Have you seen him? Sheppard's too damn weak to harm a fly!"

"Be that as it may, I can't allow you to place yourselves in danger. We don't know what Sheppard's capable of. Now, please, don't make me repeat myself…"

"That's it! You're really are paranoid! His hands are restrained, Colonel, he's still in a stasis pod, he…"

McKay's voice was drowned out by a roaring sound in his ears. Sheppard started to feel more confused. He tried to move his hands but for some strange reason, couldn't seem to do much. Everything still felt too numb and cold…. None of this made any sense; it almost seemed as if he wasn't trusted, treated like a prisoner by his own people... Confusion rained down on him again. No, it can't be true… My people … my team won't do that to me… They know me… They trust me… as I trust them… especially if they are real… God, I hope they are real… But none of this makes any sense. No hallucination can seem so real… A dream, I must be dreaming… It can be nothing else... He did not even realise that he had just refuted himself. The pain spikes in his head grew sharper. He groaned again, trying to shake his head, trying to brush them off. He felt gentle hands on his shoulders.

"Colonel Sheppard, what's wrong? Where does it hurt?" a Scottish voice asked.

He could not answer the voice as he was unable to keep his eyes open any longer, so he let the darkness claim him once again.

---

"He's fallen unconscious," Beckett stated worriedly. "Let's get him back to the infirmary before his condition deteriorates again. I don't like what the readings are showing me. His blood work is a mess. There are so many thing wrong with him that I can't even begin to guess what's been done to him."

As they began pushing the stasis pod hurriedly through the corridor, Weir made her way towards Caldwell, her features cold and angry. "What the hell was all that about, Colonel?! John did not need to hear your doubts about him in his first awakening moments of consciousness! He needs to know that he's among friends, people who care about him! Not to feel as if he's a prisoner again!"

Caldwell seemed slightly taken aback by her outburst.

"I was only doing my duty ma'am. According to Dr Beckett, Sheppard's DNA has been drastically altered. If I recall correctly ma'am, the last time something like this occurred, he took down our men who were sent after him and even attacked you."

Weir's eyes narrowed. "Are you referring to the time when John was suffering the effects of the retrovirus?"

Caldwell nodded. "Yes ma'am. I was there, I heard the reports; the stunners that the guards used on him had no effect. He had amazing agility, strength and speed. He climbed up walls, for heaven's sake! If Ronon hadn't caught him then, he would have escaped and probably killed someone, and that was when he was under the influence of Beckett's retrovirus, an accident that was not meant to happen!"

At Caldwell's words, nobody noticed Carson stiffened with guilt as he closed his eyes and took a deep breath. But he said nothing except to purse his lips tightly together and hurry faster to the infirmary.

"We are now in a whole new ballgame," Caldwell continued. "This is Wraith technology that we're talking about here. Regardless of how you see it or refuse to see it, Sheppard, in my book is dangerous and should be treated as such."

"That occurred almost a year ago, Colonel!" Weir argued back. "It's an entirely different matter! And the reason why he escaped was because I gave him no other option, no hope, no way out! Did you know that he wanted me to give the order to kill him, Colonel? The last time, when I visited John in his quarters, when I informed him that Carson and his team had failed in their mission to get what they needed to help him with the retrovirus. He had looked at me with desperation in his eyes; he understood what I was trying to say. He understood that we were just going to stand by and watch as he transformed and lost his mind turning into something that was no longer human. That we couldn't do anything else to stop what was happening to him. I told him that I was not sending anymore of our men out to get what was required, that it was too dangerous, despite him requesting me to do so. He offered to go himself, but it was something that I also denied him. We were condemning him to a death sentence in a slow and painful manner where he would become a danger to himself and those around him and John knew it. He was left with no other option, so I ask you to answer me, Colonel, if you were in his place, what would you have done?"

To her relief, she saw that she got to him, that her words broke through Caldwell's hard exterior. The Daedalus' commander appeared stunned and shocked at hearing what she had to say. When he next spoke, he looked a little loss for words; the stubborn heat in his eyes had subsided slightly. He finally cleared his throat, muttering softly, "I did not know that, ma'am."

Elizabeth sighed. "Well, that is the man whom you are accusing of being compromised, Caldwell! I'm not saying that you wanting to protect Atlantis and our personnel is wrong, Colonel. In fact, I can see where you're coming from, and I agree with you in some aspect that we should take some precautions until we can determine how to help John. But what I'm saying is that we should do it with compassion and understanding. Colonel John Sheppard deserves at least that much after what he's done for us and what he's been through."

Caldwell looked truly chastised now, his face turning a soft shade of red. He nodded looking at Sheppard's stasis pod. "I'll order that the restraints be removed, at least while he's still unconscious in the infirmary."

Weir pursed her lips and nodded. "Thank you, Colonel." It was a start. When John regained consciousness again and was a little more coherent, she hoped to be there to explain to him why he was to be placed in restraints. She hoped to God that he would understand. But at least for now, she had won this battle with Caldwell.

---

They had gone quite a distance, almost reaching the infirmary, when Beckett noticed a change in Sheppard's condition. "Wait!" he shouted out.

"What?" asked McKay anxiously. "What's wrong now?"

Beckett looked at the scanner's reading. "Quickly, move the stasis pod back to where we were before."

"What?! Are you nuts?!" McKay gasped. Teyla and Ronon glanced at each other, looking puzzled and concerned.

Beckett however ignored him as he pushed the stasis pod back with the help of his two medical personnel who didn't question his orders.

"What's going on here, Carson?" Weir asked, looking just as concerned and puzzled as the rest of Sheppard's team.

"I'm not certain yet, but I need to test something out…" Beckett replied, breathing a little harshly. "Please just bear with me here." There was determination in his voice. Weir nodded and allowed the doctor to push the stasis pod back down the corridor again.

After some time back-tracking, he called them to a halt. McKay by now had come to study the Asgard scanner readings that held Beckett's attention. "Okay, medicine is not my thing, but am I seeing what I think I'm seeing?"

Beckett looked up at him. "Aye," he replied, "Whatever we have over here, this section of the city appears to be helping Colonel Sheppard's condition to improve somewhat. When we move him further away from here, his condition starts to fluctuate slightly, certainly not to the extent when we were on board the Daedalus, but it is still there." He turned to everyone there. "So, what is here that's different from the infirmary or the Daedalus or from the rest of the Atlantis?"

Sheppard's team looked at each other.

"Could it be his ATA gene? His connection to the city, perhaps?" Weir asked.

McKay shook his head. "A good hypothesis, Elizabeth, but I don't think so. No, if it were, it wouldn't matter where he is. Any part of the City would be fine."

Telya however was frowning, looking disturbed by all of this. "It's the Wraith," she finally spoke up. "I can sense its presence strongest here."

"What?" McKay said. "Here, hold this, and don't drop it for goodness sake!" He pushed the box he held into Elizabeth's startled hands before ripping out the tablet PC that was velcroed behind his vest, swiftly switching it on. Weir looked like she was about to open the box when Rodney suddenly placed his hand on top of it.

"Sorry, Elizabeth, my mistake!" He turned to swiftly hand the tablet PC to a surprised Beckett to hold for a moment, before grabbing the box back and placing it into Ronon's hands. "Here, Conan, you hold it, you may as well be useful."

Weir looked surprised by it all but was not given a chance to say a word before McKay had the tablet back in his hands again, bringing up the schematics of Atlantis' layout.

"Hmm, let's see… Oh my, Teyla's correct! From where we are, I'll say we're relatively close to where the confinement cells are, though you might not know it from the round about way that you have to get there."

"So, what are you saying, Rodney? Are you saying that Colonel Sheppard's improvement is because we have a captured Wraith nearby?" Beckett asked, looking seriously disturbed by this piece of news.

McKay shot a look in Caldwell's direction. He knew how this was going to look to the Daedalus commander and he felt as if he was just about to stab Sheppard in the back. But he had no choice in the matter, especially when the evidence spoke for itself. "It's the only theory that we have at the moment."

"Then I say we test it out." Caldwell spoke up suddenly.

"What? How?" Beckett asked, looking wide eyed and not at all comfortable where this was heading.

Caldwell pursed his lips together. "If Sheppard needs the Wraith in order to survive, get some men to bring the Wraith captive down to the infirmary. I'll have a guard stationed by the Wraith to watch over him. If what you say is true, Dr McKay, then Sheppard's condition should improve."

---

To be continued