Chapter 5: Healing.

Carson watched the monitors with horror, John's intracranial pressure was continuing to rise and he knew that if he moved him it could kill him. But if he didn't try and move him it wouldn't matter anyway because the nanites would take over his system and he'd have to kill him.

Another thought struck him while he was staring at the monitors; could the nanites actually heal John's brain and what if eliminating them killed him.

He shook himself to get those thoughts out of his head because he knew that the safety of Atlantis was paramount.

A gentle voice interrupted his thoughts, jolting him into action, "Dr Beckett what is going on?"

"Dr Keller I need your help to get Colonel Sheppard to the chair room and into the chair."

"But moving him may kill him, his intracranial pressure is getting too high, we may have to perform surgery soon."

"I know, but this may be the only way to eliminate the nanites in him and Elizabeth."

"Alright, Carson, I'll get a medical team and a gurney ready." She suggested and he was relieved that she did it without too many questions.

He watched her leave and turned back to his patient again and he was surprised to see that John's eyes were open, which was a total surprise because given the condition his brain was in there was no way he should be conscious.

"Carson," he whispered, his voice sounding slurred.

"John, how are you feeling? Dr Keller will be here in a moment with a gurney and we will take you to the chair room."

"Carson…my…head…hurts…and…I…can't…. see."

"I'm sorry lad, but your brain is swelling again. But don't worry we'll have you in the chair room in a jiffy." Carson stopped and thought for a moment, before continuing, "are you sure it was Atlantis speaking with you and not the nanites?"

"Yeah…I'd…know…if…it…was…the nanites…. their…a…sadistic…bunch…. but…Atlantis…is kind and…loving."

"Alright lad, I believe you."

John was quiet and Carson didn't miss the tears brimming in the corner of his eyes.

"Go back to sleep lad and hopefully when you wake up you'll be feeling better."

Carson watched as his patient lost consciousness again and he wondered if his friend would ever wake up.

OOOOOOOOOOOOOO

John was bolted awake by movement, why am I in a car and why is it moving so fast, is fletcher taking me somewhere? His brain was fuzzy and garbled as he tried to comprehend what was going on. The last thing he remembered was telling Carson to take him to the chair room, for what purpose he had no idea.

The pain in his head had reached an all-time high and it felt as if someone was chopping his brain in half with an axe. The motion wasn't helping his stomach either and he felt as if he was going to be sick at any moment.

Moaning he tried to roll onto his side hoping that it would get someone's attention.

A soft lilting voice pervaded his senses, "Colonel Sheppard, please try and remain still. Your brain is swelling to dangerously high levels."

"Sick," he managed to choke out as the bile began to rise to the back of his throat.

Gentle hands rolled him on his side just in time to empty his stomach of its meagre contents.

Once he had finished retching, he was relieved to be rolled onto his back again and when the movement began again he closed his eyes. Not that it made much difference because he couldn't see when his eyes were open anyway. But for some reason having his eyes closed seemed to help his stomach.

He must have lost consciousness because he was sitting in the chair when he awoke again.

"Are you with us Colonel, "Carson asked and John could sense that he was hovering.

"Yeah," he whispered through the pain that was emanating from his brain.

"You're sitting in the chair so can you manage to contact Atlantis?"

"I'll give it a go," he whispered, knowing that it would probably use the last of his strength, but if he didn't Elizabeth would die and it was his job as a soldier to protect her at all costs even if it meant sacrificing his own life.

Putting his hands on the sensor pads he leant back and immediately heard the soft humming of Atlantis. Even though he could always hear the gentle hum of the city, for some reason it always felt stronger when he was connected to her from the chair.

He concentrated the best he could even though he could feel the immense pressure of his brain pressing against his skull, which made him think that his brain was ready to explode. So, he knew that he needed to complete his task as quickly as possible.

Moaning he went deeper into Atlantis' systems and settled into her gentle embrace and he immediately felt better.

"Are you there Atlantis?"

"I am here John Sheppard."

"What must I do to eradicate the nanites."

"You don't need to do anything; I will do all the work."

For the first time since he'd arrived, he began to relax and it wasn't long before he felt a warm tingly feeling envelop him from head to toe. He hadn't felt this good for a long time and he longed to stay in Atlantis' embrace forever.

Suddenly a sharp pain shot through his temple and he screamed and he felt his head was going to be ripped apart. Images of the last few days flashed before his eyes, Dr O'Neill was there as his doctor in the hospital, his mother was there speaking to him in a gentle voice and Dave and his father were there too. The images morphed into Fletcher and the Electro-shock therapies that he'd had to endure and finally, he was sitting by Elizabeth's side encouraging her to keep fighting.

The pain was so intense by this time that he thought that he was going to die, but at least he knew that he would die saving Elizabeth.

As abruptly as the intense pain had begun, it ceased and he felt Atlantis' soft warm embrace again.

"Atlantis," he whispered trying to catch his breath.

"I am here John Sheppard. I have eliminated the nanites from your system and I have downloaded a program for your Dr McKay to deactivate them in Elizabeth's body. I can't eliminate them from her because she doesn't have your ancient DNA."

For the first time since he'd been with Atlantis, he realised that his head was feeling much better, "have you healed my head Atlantis?"

"I have healed your brain and the skull fracture, but your optic nerves are still irritated, so it may take a few days before you are able to see again. You may still feel weak for a week or two, but in time you will be back to normal."

"Why couldn't you heal my eyes too?" He asked in confusion.

"You were so weak that if I healed you any farther, I may have killed you and everyone here needs you more than you could possibly imagine."

"Will I see you again?"

"In time, but for now your friends are waiting and they are extremely worried about you."

"Goodbye Atlantis."

John found himself falling as the gentle hum of Atlantis slowly disappeared.

OOOOOOOOOOOOOOO

Carson sat next to John watching the monitors that were still attached to his forehead and he wasn't happy, his intracranial levels had reached critical levels and if he didn't operate soon it was a strong possibility that they would lose John.

Suddenly, he screamed and it was the most disturbing thing that he had ever heard. He was almost convinced that John Sheppard was going to drop dead before his eyes. John's breathing became erratic and he was obviously in agony, but he had no idea what to do for his friend. Was Atlantis eliminating the nanites, or was something else happening?"

Then John was still and Carson watched as his friend's breathing evened out, he looked over at the monitors and was shocked to see that John's intracranial pressure was back to normal. He knew that once John was back in the infirmary the first thing he was going to do was to get him under the scanner.

A whispered voice interrupted his thoughts, "Carson, there should be a file for Rodney with instructions on how to deactivate the nanites in Elizabeth's body."

Carson looked over at Rodney, when Rodney nodded at him he turned to John, "we have it,

Colonel Sheppard. Perhaps you should go back to sleep now and when you wake up you'll be back in the infirmary and feeling much better."

"Thanks, Doc."

Carson watched as his friend lost consciousness again and if Rodney and Ronon hadn't been quick he would have fallen out of the chair and face planted.

He immediately started to bark orders at his medical staff that were standing around, "we need to get Colonel Sheppard back to the infirmary straight away, when we get there I want him under the scanner to perform a scan on his brain."

Five minutes later they were heading towards the infirmary, he was still incredibly worried about John and he knew that he would be until he got him under the scanner. Before he checked John out, he really needed to send Jennifer to the isolation room with Rodney to supervise him, while he run the program to deactivate the nanites in Elizabeth's body.

OOOOOOOOOOOOOOO

The next time Elizabeth became aware she was standing on the East pier again, but this time she was alone. It was mid-afternoon, the sun was glinting off the ocean and the sky was a brilliant blue. The spires were more alluring than she remembered them, and she felt an incredible sense of peace. She turned her head to look for John in the place she'd seen him the last time she was here, and she was surprised that he was looking at her and smiling and waving.

Slowly John faded away and she wondered whether she would see Fletcher when she turned around again. Before she had a chance to turn Atlantis and the ocean slowly started to fade away and it wasn't long before she heard voices. One of them was talking rather loudly and one of them had a soft lilt to it and she instantly recognised both of them.

Opening her eyes, she spoke as loudly as she could, "hey."

"Hey yourself," Carson said while grabbing her wrist and taking her pulse.

"It's good to see you awake Elizabeth, I'll go now and let Carson practice his voodoo medicine on you."

Elizabeth watched as Rodney waved and left the room and he appeared to be in a hurry, but that was nothing unusual for him.

"What happened?" She asked turning to look at Carson again.

"We have deactivated the nanites again and for now that's all we can do. Rodney is researching a way to eradicate them completely, but it may take some time."

She nodded, feeling relieved that it was over for now, "how long have I been asleep?"

"It's been two days since we ran the program to deactivate the nanites and before that, you had been unconscious for about five hours."

"And how is John?"

Carson sighed and she could tell that he was exhausted.

"He still asleep, but because of his ancient gene he was able to connect with the Atlantis AI and she was able to eliminate the nanites from his system."

She felt relieved that he was still alive, but if she remembered correctly he'd had a head injury the last time he was awake, "how's his head?"

"The bleed on his brain has stopped completely and his intracranial pressure is back to normal, so basically his brain is back to normal size."

"Do you know if there's any brain damage?" She asked suddenly feeling concerned.

"I don't believe so, the only problem seems to be some temporary blindness, but that should right itself within a few days."

"That's great news, Dr Beckett, when can I see him?"

"I want to keep you here for another twenty-four hours and I should be able to release you to your quarters tomorrow morning."

Now that she knew John was safe she suddenly felt exhausted again, but there was one nagging question that she needed to ask, "Was anyone else infected?"

"No, and once we discovered that the nanites were hiding behind the Colonel's ATA gene we were able to work out a way to test the other ATA gene carriers and none of us was infected. Apparently, the nanites thought it would be a good idea to convert you and John first and then they would spread to the rest of the population."

Elizabeth sighed, "that seems like a pretty stupid idea, I would have thought they would have been smarter. They were definitely arrogant but obviously stupid."

"Aye love I agree, now how about you get some rest and I will bring you some dinner a bit later."

"Thanks, Carson."

"You're welcome Luv," Carson touched her on the shoulder, she felt the warmth of his smile when he looked down at her and for the first time in a few days she actually felt warm.

OOOOOOOOOOOOOOO

Teyla sat holding John's hand and talking to him gently. It had been four days since the nanites had been eliminated and still, he slept. Elizabeth had been released to her quarters the day before and Carson had announced that she was 100 percent healthy. On numerous occasions, Carson had also assured them that John was also 100 percent well and nanite free.

Rodney and Ronon had come and gone over the last few days but seeing as Ronon couldn't sit still for long Carson had thrown him out on more than on occasion. As Rodney couldn't keep quiet or sit still Carson had thrown him out of the room as well.

Thinking back to what had gone on over the last few days she shuddered when she thought of how close they had come to losing John and Elizabeth. Carson had told them how close he'd come to activating an EM pulse to wipe the nanites out. He has also told them if Atlantis hadn't healed John's brain, he may still have died and even if he'd survived, he would have been severely brain-damaged.

Her thoughts were interrupted by a moan coming from the bed and when she looked down, she was surprised to see John looking up at her.

"How are you feeling John, would you like a drink of water?"

"Why are you blurry?" He asked with a pained expression on his face.

"How about I go and get Dr Beckett and he can explain to you what is going on?"

She took one last look at John, whose eyelids seemed to be closing already and rushed out of the room, looking for Carson.

She really hoped that it was good news that his vision was beginning to become clearer because the last thing they needed was a vision-impaired military commander.

OOOOOOOOOOOOOOO

The next time John became aware of the world around him his sense of hearing was the first to return and a loud voice complaining was the first thing that he heard.

"Carson why is he still asleep, except for the three minutes he was awake when Teyla was in here, all he's done for the last six days has sleep? Surely even Colonel Calamity doesn't need that much sleep."

He kept his eyes closed, trying not to let Rodney and Carson know he was awake. If all they were going to do was argue he'd rather still be asleep.

Carson was forceful, but quiet when he replied, "as I have told you on many occasions over the last couple of days, sleep is the good thing for him right now. He suffered massive head trauma and was infected by nanites, he isn't going to get over this quickly."

Time to wake up, he thought. I really need to get on with it and besides, I really need to know how Elizabeth is.

He opened his eyes slowly and looked in the direction of his friends and was surprised to see that his vision was near to perfect again, "how can anyone sleep with all that noise going on."

"It's about time you woke up sleeping beauty," Rodney said, and John didn't miss the sarcasm in his voice.

"It's good to have you back Colonel, how are you feeling?" Carson asked softly.

Before he had a chance to answer, Rodney patted him on the shoulder, "I'm heading back to my lab Sheppard, I'm researching a way to eliminate the nanites from Elizabeth's body."

"Catch you later McKay."

Once Rodney had left, he turned to Carson again, "did you manage to deactivate the nanites in Elizabeth?"

Carson nodded, "yes, thanks to the program the Atlantis supplied, but we still want to eliminate them from her body."

"If anyone can figure it out Rodney can."

"Are you going to answer my question now Colonel, the one I asked when you woke up?"

He sighed, considering what he'd been through, he didn't feel too bad, "my vision's still a bit blurry, but other than that I just feel tired."

"Your optic nerves a still a bit irritated, so that should right itself in a few days. You were lucky that Atlantis was able to heal your brain injury, otherwise, you could have died or at the very least you would have been severely brain-damaged."

He sucked in a deep breath when the realisation hit him, how serious his latest injury had been.

"What caused the skull fracture and subdural haematoma, was it the nanites or did I do it when I hit my head on my bedside table," he paused before continuing, "I have no idea why I remember hitting my head because surely short-term memory loss is a common occurrence with a head injury?"

"Ronon tells me that you hit your head in the gym a few days before that as well, that could certainly have contributed to the injury." Carson looked at him with a serious look before he continued," I wish you would tell me when you hurt yourself Colonel because one day, I may not be able to patch you up and I'm positive that Atlantis won't always be there to heal you."

He felt severely chastised by the doctor, but then perhaps Carson was right, maybe he needed to look after himself. After all, Atlantis had told him that the inhabitants of Atlantis needed him.

"I'm sorry Carson. I will try harder to look after myself."

"That's all I ask Laddie, but for now I think you should try and get some more rest and before you ask, I will release you the day after tomorrow. I would like to get you on your feet tomorrow to make sure that you can walk without too many problems since you have been unconscious or asleep for nearly two weeks."

He nodded and was surprised that there was absolutely no pain in his head at all, but he had one last question to ask Carson before he went back to sleep, "Carson why were the nanite infecting me so stupid? They seemed to be intent on creating a fake world for me one minute and the next they seemed to be telling me they wanted to take over Atlantis using me and Elizabeth."

"I believe that it has something to do with your ancient gene, but that's just a guess. I've asked Rodney to research it more," Carson smiled at him before continuing, "apparently, he's even asked Radek to help him."

John chuckled; it was extremely rare for Rodney to accept help from anyone. "I'm beginning to feel sleepy again Doc."

Carson patted him on the arm and turned to leave the room.

"Hey Doc," he called out, hoping that Carson would turn around again and when he did, he continued, "thanks for everything."

"You're welcome son," Carson said, before turning around again and leaving the room.

Once his friend had left, he closed his eyes and thought about how lucky he'd been this time, if one little thing had been different over the last few days, he knew that he'd probably be dead by now. He now knew that he had a guardian angel watching over him and her name was Atlantis.

OOOOOOOOOOOOOOOOOO

Elizabeth took a deep breath as she entered the mess hall, it was lunchtime and she assumed that John would be there. She hadn't had a chance to talk to him since he'd woken up and been released from the infirmary. She'd been in to visit him the day after her release from the infirmary and she'd even sat with him for a while, but he hadn't woken up.

For the last two day's she'd been too busy in meetings with the SGC and catching up on paperwork, so she simply didn't have time, at least that was what she was telling herself. Truth be known, she had no idea what to say to him, he had saved her life yet again. What do you say to someone who feels that it's his duty to lay down his life for everyone else, without any concern for his own wellbeing? Perhaps she should tell him that it has to stop, and he needed to think of his own welfare, but she knew that Carson had already told him that and as usual, he'd told Carson he was a soldier and protecting people is what he did.

Looking around she spied John sitting at a table by the ocean. She knew that he would be alone as Teyla and Ronon were off-world with Lorne's team and Rodney was in his lab as usual. She had no idea where Carson was, but she hoped that he would be getting some rest since he'd spent most of the last two weeks in the infirmary.

She chose a sandwich and a piece of fruit and took a deep breath before heading over to see John.

"John it is good to see that you're finally out of the infirmary."

He looked up at her and she could see the dark lines around his eyes. It was clear that the last two weeks had taken a toll on him.

"Oh hey, Elizabeth, do you want to join me?"

She sat down across from him and he just went back to staring at the food on his plate.

"How are you feeling John?"

"I'm good," he replied, using his standard response, "how are you?"

"I'm feeling much better thank you."

She looked down at the food on her own plate and thought, this conversation is going nowhere fast. It's about time we talked about what happened and whether he wants to or not, I need to talk about it.

"John, I need to thank you for what you did for me. Carson said that you almost died when you were connected to Atlantis. That was a big risk you know because you had no idea whether it was the nanites or Atlantis trying to get you into that chair. Believe it or not, I cut crook at Carson for allowing it."

He looked up at her and smiled, "I don't think connecting with Atlantis is what almost killed me. Carson said that it was a combination of the head injury I suffered and the seizures I had every time Fletcher tried to fry my brain and believe it or not, I knew that it was Atlantis and not the nanites. I can't explain how right now, but I just knew."

That took her totally by surprise as she had no idea what, he'd gone through with the nanites, "what did they do to you?"

He chuckled nervously, "electroshock therapy, which caused seizures, which in turn aggravated my existing head injury."

"Oh, John I'm so sorry that you had to go through that."

"Don't worry Elizabeth it all worked out in the end. My brain and head are healed I can see again and we're both free of nanites."

She knew that he didn't really want to talk about it, so she let the matter drop for now and decided to tell him about her meeting with the SGC.

"I have just spent all morning talking with the SGC, they wanted to know why they weren't informed about the nanite crisis. Lorne, Rodney, and Carson were there as well, but the best part of the meeting for me was when Rodney told him we'd been having trouble with the gate for weeks. According to Rodney, it was repaired a few days ago."

She looked at John waiting for a reaction and she was relieved when his face lit up and he started to laugh. It was almost as if the weight of the world had been lifted from his shoulders. His laughter was contagious and very soon she found herself in hysterics as well.

When they finally stopped laughing, she looked at him and smiled, she knew that the events of the last two weeks would haunt them both for months to come, but they both had no choice to get over it and move on.

"When is Carson putting you back on duty?"

"I can go back on light duty tomorrow and he wants to give another couple of weeks to build my fitness up before he puts me on active duty again, but I can deal with that, I'm just happy to be alive."

She nodded and took his hand, "I have to get back to work, but if you ever need to talk, make sure you talk to someone on your team, or you'll have to talk to Dr Heightmeyer."

"I know, Carson told me the same thing and what about you, have you spoke to Heightmeyer?"

"I have already had two sessions with her and believe it or not I feel better already."

"I'm glad you're feeling better Elizabeth."

Patting his hand, she stood up to leave, "anyway I need to get back to work, I'll catch you at dinner time."

"See you later Elizabeth."

She picked up the rest of her sandwich and left the mess hall, happy that she'd finally found the time to talk to John.

ooooooooooooo

It was only 1900 hours when John fell into bed that evening, he'd spent the day trying to read and when that began to hurt his head, he had wandered the halls of Atlantis.

At 1700 hours, he'd met his friends in the mess hall for an early dinner and it was a time where he'd finally allowed himself to relax and have some fun. By 18:30 hours his eyelids were beginning to droop and Elizabeth had suggested that he should enjoy an early night while he had the chance because once he was back on duty he would probably be up until all hours of the night.

His eyes closed the minute his head hit the pillow and within five minutes he was fast asleep.

He hadn't been asleep long when a voice called to him in the darkness, "John Sheppard are you there?"

"Is that you Atlantis?"

"Yes, John it is me."

A figure approached him from out of the darkness and it was a face that he thought, he'd never see again. It was his mothers, the inky black hair, deep Hazel eyes and alabaster skin were the same as they had been before she'd become sick.

"Mom," he whispered.

"I chose this form because this woman was someone important to you. I hope you don't mind?"

"It's perfect Atlantis, I'm glad that I have been able to talk to you again."

"We will speak more often in the future now that you have the ability to contact me, but for now you must rest as your body is still healing."

He nodded as he watched Atlantis walk away from him, he knew that eventually, he would be alright, but for now, he would take Atlantis' advice and rest.

There was still much work to be done in the Pegasus Galaxy and he knew that he had a big part to play in it.

Fin…

Thank you to everyone who has reviewed and commented on this story, I really appreciate your support.