Disclaimer: I do not own Stargate or any of its characters. I do love to write about them though.

Disclaimer: I am not a Doctor or medical health care professional. Although I have tried to research medical terms, they may not be 100 percent accurate.

This story takes place straight after season three's episode, 'The real world'.

Was Sheppard really free of nanites after touching Elizabeth? What happens if he wasn't?

Chapter 1: Nanite free.

Elizabeth stood on the control room balcony overlooking the gate-room and she still felt unsettled by what had happened to her that day. Carson had ordered her to go and get some rest, but she knew that if she fell asleep, she would probably have nightmares, so she would put that off for as long as possible. She held her father's pocket watch in her hand and run her fingers over the smooth, cold metal. For now, it felt like it was anchoring her to the real world. She shuddered thinking about what had happened in the fake world that the nanites had created in her and she knew that it was something that she never wanted to experience again. She sincerely hoped that no one else would have to go through it either.

A voice interrupted her thoughts, which surprised her. It was late, and most people had retired to their quarters or gone to the mess hall a long time ago.

"Still up, huh?"

She turned to look at John Sheppard, whose hair was sticking up much more than normal and she didn't miss the dark lines under his eyes. She knew that it had been a long day for him, as he had spent most of the day outside of the isolation tent in the infirmary worrying about her.

"Oh, hey, "she said smiling, "Yeah, I wasn't all that keen to go back to sleep just yet, so I came up to my office."

"Understandable."

"I'm glad to see you've been released from quarantine John."

"Yeah, Well, I guess the nanites were too focussed on you to spread to me."

"I now realise just how insidious they really are." She said shaking her head, "I mean if such a small number of them could do that to me."

"Let's just take it as a win right now," Sheppard replied with a crooked grin.

She shuddered as she answered him, "alright. Still, I can't believe I was only out for five hours."

"Felt longer, huh?"

"Yes, A lifetime."

"Well, it's good to have you back in the real world. At least, I think it's the real world ... I could be infected right now, which makes me the one ..."

She just glared at him for that comment, "John, don't."

"Sorry."

"Anyway, I was just off to bed, but I thought that I would check on you first, so goodnight Elizabeth."

"Goodnight John."

Smiling she watched him walk away, feeling relieved that he hadn't been infected by nanites which gave her hope that life on Atlantis could get back to normal as soon as possible.

Before she had a chance to turn back and look at the gate, John suddenly grabbed his head and screamed before falling to the floor and hitting it hard. She was by his side in a split second and was shocked to see his whole body trembling and then suddenly he was so still and quiet that she almost believed he was dead. Looking at his eyes she realised that they weren't closed, and he was staring into space, she didn't miss the pain lines around his eyes either.

"John, can you hear me?" She asked in a panicked voice.

There was no reply, he just continued to stare into space for a few more minutes and then his eyes closed. She wasn't sure whether she was relieved or not, but now she could believe he was sleeping at the very least.

Sighing she tapped her earpiece and called Carson, "Weir to Beckett medical emergency in the control room."

"What seems to be the problem?"

"Colonel Sheppard has collapsed in the control room and he appears to be unconscious, before he collapsed, he started to scream and hold his head. His eyes were open for a few minutes after he collapsed though, but now they're closed."

"I'm on my way, Beckett out."

Cutting the communication, she went and sat down next to John and held his hand. What the hell's happening now, she thought, perhaps I was beginning to relax too soon.

OOOOOOOOOOOOOOO

Carson had had enough, and it had been an awfully long day on Atlantis, first trying to eliminate the nanites from Elizabeth and then making sure that Colonel Sheppard hadn't been infected with the same nanites. He had released Colonel Sheppard from quarantine an hour ago, with orders to go and eat and then go straight to his quarters to get some sleep, which was an order that he didn't expect the stubborn Colonel to follow.

In another half an hour he would be off duty and he had every intention of heading straight to bed and falling into a deep sleep and then hopefully he wouldn't wake up until morning.

Sitting down at his computer, he decided to get some paperwork done before he finished for the night, he was just about to start on the first file when his earpiece activated.

Tapping his earpiece, he was surprised to find that it was Dr Weir on the other end, "Weir to Beckett medical emergency in the control room."

"What seems to be the problem?"

"Colonel Sheppard has collapsed in the control room and he appears to be unconscious, before he collapsed, he started to scream and hold his head."

"I'm on my way, Beckett out."

Sighing he went to grab his bag having no idea how long it would be before he finally got to bed.

OOOOOOOOOOOOOOOO

John moaned as someone shone a penlight in his eyes, "go away," he mumbled, flapping his hands in the air.

"Colonel Sheppard, I need you to open your eyes for a minute?"

His garbled mind tried to figure out what was happening, I recognise that voice, but what is Carson doing in my bedroom? Slowly he opened his eyes, and it didn't take him long to remember what had happened, a white-hot pain had shot through his head, right before he had collapsed on the floor just outside of Elizabeth's office.

Carson's voice interrupted his thoughts again, "do you have a headache lad?"

He must have zoned out for a minute or two, because the next thing he knew was that Elizabeth was talking to him, "John, Carson is talking to you. In fact, he's asked you the same question three times now."

"Sorry Doc, what did you say," John mumbled, trying to ignore the sledgehammer that was rearranging his skull.

"I asked if you have a headache lad."

"Yeah, just a small one doc so do you have some Tylenol or something I can take for it? Then I promise I'll head to my quarters and go to bed."

"I don't think so Colonel, you will be coming to the infirmary, the only question is whether you can walk or whether I'll be calling a gurney."

"There's no way I'm going on a gurney, so if you just give me a few minutes, I'll try and get to my feet so that I can walk."

He struggled for a few minutes and was relieved when he finally managed to stand on his feet. He held on the wall to steady himself, before following Carson to the infirmary. His headache intensified the minute he started to walk, but there was no way he was going to tell Carson that. He planned to spend as little time in the infirmary as possible and then head to his quarters so that he could get a good night's sleep, he was positive he would feel better in the morning then.

He must have zoned out again because before he knew it, he had arrived in the infirmary and Carson was talking to him.

"Colonel, can you please hop on the exam bed so that I can conduct some tests."

"Huh…" he muttered after zoning out again.

"Exam bed, now!" Carson stated forcefully.

John saw the look in his friend's eyes, and he knew that he should do what Carson wanted because the doctor could be scary at times and it never paid to get on the man's bad side.

Once he had settled on the bed the poking and prodding began. Carson's penlight was shone in his eyes again and although he tried to stop it, he couldn't help but flinch.

"How's the headache John and are you hurting anywhere else?" Carson asked in a sickly-sweet tone.

He knew better than to lie outright to Carson, so he opted for minimising the truth a little, "my head still aches a little," he said trying not to let his pain show.

The truth was his head felt as if a drill was drilling deep into his brain making it difficult for him to focus. The rest of his body had developed a constant fuzzy ache since he'd arrived in the infirmary, but there was no way he was going to tell Carson that, in case Carson wanted to keep him there overnight.

"Alright, Colonel, I want you to change into some scrubs so that I can conduct a few more tests and then you'll be my guest overnight."

"Huh…" he muttered annoyed at himself for zoning out again.

"Colonel, are you having trouble hearing me?" Carson asked and John could hear the compassion and worry in his voice.

"No," he lied. Well, he wasn't really lying, he just kept zoning out. "You want me to put on some scrubs and then you want me to stay in the infirmary overnight," John replied, hoping that he had guessed correctly about the doctor's wishes.

He was happy when Carson nodded, but when he handed him the scrubs a few minutes later he scowled, which sent a white-hot pain shooting through his brain causing him to wince and put his head in his hands.

After taking a few seconds to compose himself he turned to Carson and put on his best puppy dog look, "any chance of a shower doc?"

"No lad, you're in too much pain and don't think I don't see it because I can see the pain lines around your eyes.

He sighed as Carson pulled the privacy curtain around his bed allowing him to change into the scrubs he'd been given. Once he was alone, he found that his body was trembling all over and there was a deep ache that pervaded every part of his being. Although he didn't want to stay in the infirmary, he had to admit that perhaps Carson was right, and he needed to be in a hospital bed under observation for the night.

By the time Carson opened the privacy curtain, he'd managed to change into the scrubs, but he was puffing and panting like he'd run two marathons back-to-back, and he was sitting on the floor because there was no way he had the energy to get on the bed.

"What are you doing sitting on the floor lad?"

"Sorry Carson, I suddenly felt tired and needed to sit down," he said in between breaths.

"Right then Laddie, I'll help you into the bed and then I'll give you something for the pain you're obviously in."

"Sounds good to me Carson," he agreed and let Carson help him onto the bed.

Once he was settled in the bed, he closed his eyes and allowed his breathing to even out. He would have fallen asleep if Carson hadn't come back and stuck him with an IV line.

"Hey," he protested, "what's that for?"

"You're looking a little dehydrated and don't think I can't see how much pain you're in. You're squinting your eyes into little slits, that's usually a sure sign you're in pain."

"Alright, alright, just let me go to sleep and I'm sure I'll be feeling much better in the morning."

"Okay, just let me take some blood and take a full-body scan, and then I'll give you some pain meds so that you can you to sleep."

"Thanks, Doc," he mumbled trying to keep his head still, hoping that he could stop the sledgehammer from rearranging his skull.

Ten minutes later he was relieved when Carson announced that he had finished conducting his tests, for now, so he closed his eyes and waited for the pain medication that Carson had just slipped into his IV to take effect. It didn't take long until he felt a cool soothing numbness flowing through his veins and the pain began to dissipate. His brain began to feel fuzzy, and he could feel the darkness encroaching on him, so he allowed himself to drift off into a deep peaceful sleep.

OOOOOOOOOOOOOOO

Carson sat in his office looking at the latest round of tests he'd conducted on Colonel Sheppard and he was completely bewildered at the results. There appeared to be absolutely nothing wrong with the man and he had no idea why he had collapsed. He had checked for nanites three times now and John was clear, so he was positive that they weren't causing John's problems. He couldn't find any unknown viruses or bacteria in his blood and there was no evidence of a brain or head injury. He wondered whether John was simply suffering from stress. Life on Atlantis was dangerous at times, so perhaps all that John needed was a good vacation, perhaps he'd suggest it when he released John from the infirmary.

He sighed and wondered whether he should just head to bed, he had no idea what the time was, but he suspected that an hour or more had gone by since Elizabeth had called him to the control room.

"How is he, Carson?" Elizabeth asked interrupting his thoughts and entering his office.

"I believe that he may be suffering from a migraine brought on by stress. You know how hard he likes to push himself and I know how worried he was about you today or was it yesterday. I have no idea what the time is or how long Colonel Sheppard has been here."

Elizabeth smiled at him making him blush, "I believe that Colonel Sheppard is not the only one who has been pushing himself too hard, so I suggest that you head to bed and make sure you have a good night's sleep. There are plenty of good doctors on Atlantis to keep an eye on Colonel Sheppard and for your information, it is after midnight."

"Aye, I think you're right about heading to bed and when Colonel Sheppard is released, I would like to take him off of active duty for a few days."

"I think that it's about time we ordered some time off for everyone so first thing in the morning I will draw up a roster to make sure everyone has a vacation," Elizabeth told him and Carson didn't miss the dark circles underneath her eyes.

He was about to head to his quarters when Teyla, Ronon and Rodney came bursting into his office, "what can I do for you three?" He asked trying to remain patient.

"Is it true that Sheppard collapsed in the control room, what is wrong with him, have you been able to fix him with your voodoo magic?" Rodney ranted his words tripping over themselves.

"I believe that he has a migraine, so for now all I can do is keep his room dark and we all need to keep quiet around him," Carson replied as firmly as he could without shouting.

"Thank you for letting us know what is going on Dr Beckett, we will leave the infirmary now and all head to bed," Teyla said to him and she sounded more like a kindergarten teacher than the fierce warrior that she was.

"Really, Teyla, I wanted to see Sheppard, before I left and when I do leave, I have no intention of going to bed, I'm heading to my lab," Rodney told her and Carson could tell that the scientist wasn't happy.

Carson took a deep breath before replying, "no-one will be seeing Colonel Sheppard and I don't care what you do when you leave here, but I will most definitely be going to bed."

Before Rodney had a chance to open his mouth again, Ronon grabbed him by the arm and dragged him out of the room.

"Goodnight Dr Beckett, Dr Weir," Teyla said softly before she followed Rodney and Ronon out.

Carson breathed a sigh of relief, the last thing he needed tonight was Rodney being difficult, "I think I'll take one last look at Colonel Sheppard and then I'm off to bed. Dr Cole is on duty tonight, so I know he'll be well looked after."

"Goodnight Carson," Elizabeth said before leaving his office.

Once he was sure that she'd left, he closed his computer and left his office. He was happy that Colonel Sheppard was sleeping peacefully when he checked on him a few minutes later so he checked his vitals one last time, and he was relieved to see that everything seemed normal. Once was sure that the lights were dim enough, he left his friend in the hands of his staff and headed to his room hoping to get a good night's sleep.

OOOOOOOOOOOOOOO

When John awoke again there was sun streaming through the small infirmary window and he was surprised that he felt much better than the night before. He wondered what time it was and whether Carson would let him leave today.

Shuddering he remembered what had happened the day before and he hoped that they would never have to deal with the replicators or their nanites ever again, but he also knew that life in the Pegasus galaxy was never that simple, so at some point, they would show up again. The replicators were just another bunch of intergalactic bullies and like the bullies he'd fought in grade school, they wouldn't disappear easily.

He turned his head to the side and realised that Elizabeth was sitting beside him reading a book.

"Good morning Elizabeth, "he whispered his throat feeling as dry as the Sahara Desert.

"Good morning John, how are you feeling this morning?"

"Better. Although I'm still feeling a little tired and I could definitely use a glass of water."

She poured him a glass of water from the jug that was on his bedside table and when she handed it to him, he was surprised to see how much his hands were shaking. If she noticed she didn't mention it, much to his relief.

"I'll go and get Carson as he wanted to know when you were awake."

Watching her leave made him feel tired again so he closed his eyes and leant his head back against the pillows.

"How are you feeling this morning Laddie?" Carson asked entering the room and unfortunately, his voice was loud and irritating. Even though he felt much better, his head was still sore.

"I'd be much better if you kept your voice down."

"Is your head still hurting Colonel?" Carson asked speaking in a much softer tone.

He was about to reply when Elizabeth patted him on the shoulder, "I have to go and do some work, but I'll see you later."

He smiled at her as she left the room, "I'll see you later Elizabeth."

"Right, laddie, let's check your vitals and if I'm happy by what I see I'll give you some Tylenol and you can go to your quarters and rest up for the day."

Feeling incredulous by what Carson had just said to him, he opened his mouth and started to complain, "Carson I don't need to rest up, I have work to do."

"I am relieving you of your duties and ordering you to your room to rest for the day and if I find you in your office, or Elizabeth's office, I will sedate you and drag you back to the infirmary, do you understand!?"

Carson had gone into scary mode again, so he knew that he had to say something to placate him, "Okay, doc, but can I get some breakfast first?"

"I will ask Teyla to bring you something and then I want you to rest this morning. I will come and check on you in your quarters at lunchtime then."

"That sounds like a plan so can I get changed now?" John asked using his best puppy dog eyes to try and calm the scary doctor down.

He was instantly relieved when Carson nodded and went to collect his clothes. Sitting up on the bed he was happy when the world didn't start to spin, and his head didn't explode.

When Carson returned with his clothes a few minutes later he was ready to get dressed. Carson smiled at him and told him that he would be back in ten minutes. He had just taken his scrub pants off and was about to put his track pants on when Teyla opened the privacy curtains and entered.

"Hey!" He exclaimed feeling embarrassed as he tried to pull his pants up as quickly as possible.

"Do not worry Colonel, my people live in large tents and are used to seeing each other half undressed."

"You may not be embarrassed but I am so can you please leave until I call you back?"

She looked him up and down and smirked before backing out of the area, leaving him in peace to dress.

Five minutes later he opened the privacy curtains to find that Teyla was sitting on the next bed talking to Carson.

He was instantly worried when he saw Teyla sitting on an exam bed, "Is she alright?"

"She is fine," Carson told him, "I am giving her a list of instructions so that she can keep an eye on you when you get home."

"I'm a grown man Carson, I think I'm quite capable of looking after myself."

"Yes, John, I know that you are quite able to look after yourself, but I would like to help you. Can you please let me do that?" Teyla asked soothingly.

How was he supposed to argue with her when she spoke in such a loving gentle tone, "alright can we go now?"

"Off you go then," Carson said shooing them out the door.

John followed Teyla out of the infirmary and he felt better than he had all morning, he still had a slight headache and his body still tingled all over, but other than that he was happy to be out of the infirmary and headed back to his quarters. According to Carson, he'd had a stress-related migraine. When he'd asked Carson whether the nanites had infected him, Carson had assured him that he was definitely all clear.

It didn't take him long to realise Teyla was walking towards his quarters, "hey, Teyla can't we go to the mess hall for something to eat?"

"Rodney and Ronon will be joining us shortly in your quarters and they will be bringing food with them as per Carson's orders."

All he could do was groan at the suggestion because he knew that there was no way Teyla was going follow his suggestion and let him go to the mess hall.

"You know what Teyla, I think I can find my quarters without your help and can we skip the breakfast since I'm suddenly feeling extremely tired."

"Are you sure John?"

"Yeah, why don't you come by in an hour with some food?"

"Alright, but please let me know if you need anything."

She turned and left, much to his relief. His headache was notching up again and he definitely felt exhausted so perhaps a morning nap would be a good idea.

By the time he arrived at his quarters, his body was aching from head to toe and his brain felt like a thousand white-hot needles were drilling into it. Staggering into his room, he locked the door behind him and stumbled towards his bed. Suddenly a bright yellow light flashed in front of his eyes and the pain in his head intensified tenfold.

He grabbed his head and screamed while still trying to make it to the bed, but he never made it as he collapsed in the middle of his room, hitting his head on the bedside table before he hit the floor. Within seconds of landing on the floor, he was unconscious.

TBC…

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