Chapter 2: What is going on?

John slowly became aware of his surroundings when he heard voices in the distance, he had no idea where he was, but the one thing he did know was that his head was pounding, and he ached from head to toe. The bed he was laying in was soft and he could smell disinfectant, so it was a good bet that he was in the infirmary. He opened his eyes to try and see what was going on around him and was surprised to find that it was pitch black. Perhaps it's the middle of the night in the infirmary, he thought before thinking on, hoping that the lights would come on.

When nothing happened, he tried again, and he was shocked when still nothing happened. What the hell is going on. He was really beginning to despair by this time, was there something wrong with his ancient gene, or maybe he wasn't in the infirmary at all.

He tried to recall the last thing he was doing before he'd woken up here, but when he tried to remember the pain in his head intensified. Moaning he grabbed his head and started to pull at his hair, hoping that the thousand tiny needles digging into his brain would disappear. His body wasn't feeling much better either as the ache he was feeling suddenly escalated to the point where he was in excruciating pain.

Between the waves of pain that were enveloping his head and body, he heard the footsteps of several people running towards his bed. He really hoped that it was Carson and his team, but for some reason, he suspected that it wasn't.

"Carson," he whispered jumping when someone touched his arm.

"No John it's Dad and you're in a military hospital back in the States."

Okay so if I'm back in the states why the hell is my Dad sitting with me, we haven't spoken in years? Was his first thought and the second was, why the hell am I not is the infirmary under Carson's care?

"Why am I not on Atlantis?" He asked through gritted teeth as the pain intensified again.

A voice he didn't recognise entered the conversation, "Major Sheppard you were involved in a helicopter crash in Antarctica three weeks ago and you have been in a coma until today. You were in a bad way when you arrived back here and there was a number of times when we thought that we'd lost you."

"Who the hell are you and why am I not on Atlantis under the care of Carson Beckett? And it's Lt Colonel to you," he hissed through the pain, he was not in the mood for practical jokes so he wished these people would stop messing with him and tell him the truth.

"I am Dr Jack O'Neill and I have no idea where Atlantis is, but you have been flying helicopters in Antarctica for the past year."

John was incredulous by this point, "General O'Neill what the hell do you mean you're a doctor and why the hell can't I see?"

For the first time, he recognized the General's voice and it made him even more confused because O'Neill shouldn't be here anymore than he should.

Although John's eyes weren't working his ears were working fine, so when the doctor whispered to someone in the room, he heard every word, "I believe he has hit his head harder than we thought, I suggest we arrange a visit from a psychologist?"

He was really beginning to feel worried by this time, Carson had obviously got it wrong, and he was infected by nanites. But for now, he needed to keep his mouth closed and find out what was going on.

"Okay, Doc what's the damage?" He asked rubbing his head to try and alleviate the constant drilling going on in his skull.

"You hit your head rather hard causing a subdural haematoma, the bleed seems to have slowed, but we are still monitoring it. Your kidney and Liver were damaged causing internal bleeding which we managed to stop."

"Why can't I remember anything then?" John asked wondering whether what they were saying was true.

"Memory loss is a symptom of any brain injury as is blindness. Recent studies have also revealed that a person may create a fantasy world around them to block out the pain and loss they may be feeling after a traumatic event," the strange doctor, who claimed to be O'Neill answered.

This sounded similar to what Elizabeth was telling him about her experiences when the nanites had invaded her body, but he had been beside her then and telling her to fight. Although she had been unconscious at the time, he was sure that she'd heard him. He really hoped that someone was by his side right now and telling him to not give up.

His thoughts were interrupted by a voice that he thought he'd never hear again, "John why don't you just lie back and relax, Doctor O'Neill has just given you some pain meds to try and help you sleep."

"Mom," he whispered.

"Yes, John just go to sleep and I'll be here when you wake up."

His brain was becoming fuzzy and the excruciating pain he'd been feeling when he had awoken was beginning to dissipate. He knew that before long he'd be unconscious again, the only question was, where would he be when he woke up?

OOOOOOOOOOOOOOO

Teyla headed straight to the mess hall after she's spoken to John and she had every intention of getting him some food and heading straight back to see him. Perhaps she wouldn't ask Rodney and Ronon to join them as she suspected that John wanted to be alone. He did need to eat though, and she knew that when he wanted to be alone there were only two people who he would let in, one of them was Elizabeth and the other one was her.

Arriving in the mess hall a few minutes later she was surprised to see that Ronon and Rodney were already sitting at a table eating breakfast. They were supposed to wait for her to get there and then they were all going to John's room together, not that it mattered now as John wanted to be left alone.

She walked up to them and spoke to Ronon whose plate seemed to be piled high as was Rodney's, "why are you eating here, you were supposed to wait until I got here so that we could all eat with John?"

"Don't worry Teyla, I'll still be hungry enough to eat when we get to Sheppard's quarters," Rodney stated while stuffing a fork full of eggs into his mouth.

Teyla sighed, "Do not worry as I believe that John would like to be left alone, so perhaps I will take him something to eat."

"What's his problem?" Ronon asked her not bothering to look up from his food.

Teyla shrugged her shoulders, "I do not know, but I believe that he is annoyed at Carson for sending him to his quarters. I also think that he is still in pain and we all know that Colonel Sheppard would never admit to it."

"Maybe you should go and talk to him then," Rodney said with his mouth full of food. He finished what was in his mouth before continuing, "and I'll come by later to see him."

"Me too," Ronon mumbled looking up for the first time since she'd entered the mess hall.

"I will see you later then," she said before turning around and heading to the serving table, where she chose some eggs, bacon, and coffee to take to John.

When she arrived at John's quarters five minutes later, she sounded the door chime expecting him to answer straight away.

There was no answer, so she tried again and there was still no answer. She was beginning to become worried by this time, so she started to pound on the door," John it is Teyla I have brought you some breakfast."

Again, there was no response so she knew that there was only one thing that she could do, tapping her earpiece she contacted Carson, "Teyla to Carson come in please?"

"What seems to be the problem Lass?" Carson asked and Teyla didn't miss the worry in his voice.

"Colonel Sheppard will not answer his door so can you please use the medical override to open it?"

" Why, didn't you go to his quarters with him?" Carson asked and she could sense that he was annoyed.

Teyla felt annoyed herself, why was Carson questioning her when she was positive that John needed them, "please hurry Carson as I believe that Colonel Sheppard may need us?"

"Aye lass, I'll unlock the door from here and I'll be there in a few minutes with a medical team."

"Please hurry Carson, Teyla out."

She took in a deep breath and waited by the door, hoping that Carson would be quick. She had no idea how, but she really sensed that John was in serious trouble, which was definitely nothing new for him.

A few seconds later the door opened, and she was able to rush in. When she entered, she wasn't happy by what she saw, John was lying on his stomach in the middle of the floor and there appeared to be a lot of blood pooling around his head.

She knelt next to him and was shocked to see a large deep cut on the side of his head and there was already a lot of bruising beginning to appear around the wound site. Looking around the room, she managed to find an old t-shirt to put pressure on the wound. It was worrying when he didn't even move when she pressed the cloth onto his head so she gently spoke in his ear, trying to attract his attention, "John can you hear me?" There was no response so when Carson arrived a few minutes later, she was relieved.

"Carson, he seems to have hit his head and he is nonresponsive."

"Let me have a look at him Lassie and then I may have a better idea of what is going on?"

She watched as Carson shone his penlight in John's eyes and she was worried when John didn't even flinch.

Carson tapped his earpiece and she assumed that he was speaking to someone in the infirmary, "I'm bringing Colonel Sheppard in with a head injury, he's unresponsive so I will need you to get the scanner set up as I want to conduct some scans as soon as I get there."

She had no idea what the response was, but Carson turned to her while the medical team got John on the gurney.

"How is he, Carson?"

"I can't tell you anything until I get him under the scanner so why don't you contact Rodney, Ronon and Elizabeth and arrange to meet them in the infirmary waiting room."

After Carson had left, she looked around John's room and shuddered at the pool of blood that was on the floor, that is a lot of blood, but then Carson is always telling us that head injuries bleed a lot, perhaps it's not as serious as it seems. With that thought, she turned around and headed to the infirmary waiting room to wait for news of John yet again.

OOOOOOOOOOOOOOO

The first thing Carson did when he arrived in the infirmary was put Colonel Sheppard under the scanner and he was disturbed by the results. There was a hairline fracture in his skull, and he'd developed a subdural haematoma, which was a serious condition that needed to be monitored closely. At the moment the bleeding was slow so hopefully, he wouldn't need to operate, and the bleeding would stop automatically. Dr Cole had then stitched up the wound on the side of his head, unfortunately, they'd had to shave off some of his hair to do it.

His thoughts were interrupted when the new young Doctor came up and spoke to him, "would you like me to get Colonel Sheppard settled in the ICU while you let his friends know what is happening?"

"Thank you, Dr Keller, and can you make sure that someone is sitting with him at all times?"

"How about I take the first watch while you go and tell his friends what's going on?"

He smiled at the young doctor. Even though she was new and young, she was one of the most gifted doctors on Atlantis, and he trusted her to look after Colonel Sheppard.

"Thanks, Luv," Carson said as he watched her walk away.

He immediately turned and headed towards the waiting room. When he entered a few seconds later he found three anxious faces looking up at him.

"How is he, Carson?" Rodney asked jumping to his feet and knocking over the chair he was sitting in.

"He has a cracked skull which has led to a subdural hematoma. The bleeding is slow at the moment, but we are monitoring him closely. He has ten stitches in the side of his head and unfortunately, we had to shave some of his hair." He smiled before turning serious again, "the injury is serious, but for now he is in a critical but stable condition."

"Was this injury caused when he hit his head, Carson?" Teyla asked with concern.

"To be honest we're not entirely sure. Brain injuries can sometimes take days or weeks to show up and given the fact that he had a migraine last night he may have already been injured." Carson sighed before continuing as he had a feeling that it was going to be another long day, "does anyone remember him hitting his head over the last couple of weeks?"

"He hit the floor hard when we were training in the gym the other day and I think he may have hit his head," Ronon supplied.

"Really why didn't you send him to the infirmary?" Carson asked trying to remain patient since he already knew what Ronon's answer would be.

"He said he was fine and he didn't look injured, so I didn't push it," Ronon answered in a flippant tone.

"Idiots," Carson muttered under his breath.

"May we see him now?" Teyla asked in her usual serene tone and Carson was relieved for the change in subject.

"I think I'll head to my lab since I have so much work to do," Rodney told him, and Carson knew that it was an excuse not to have to sit with his injured friend.

"I'll catch him later," Ronon mumbled before standing up and leaving the room.

"Aye follow me?"

He'd noticed that Elizabeth wasn't there, so perhaps he would contact her and let her know what was going on before he checked on his most frequent patient again.

OOOOOOOOOOOOOOO

When Teyla followed Carson into the ICU a few minutes later, she was shocked by what she saw. John's head was heavily bandaged, and his face was as pale as the sheet that was covering him. He was incredibly still, which was a word that he never associated with John Sheppard, the man was usually so animated, and it was devastating to see him so still.

She looked over at the young doctor sitting next to John and she wondered how young she actually was, she knew that if Carson believed in her then she must be a brilliant doctor.

"Dr Keller, may I sit with him for a while?"

The young woman looked up at her and smiled and Teyla decided that when John was feeling better, she would spend some time with Jennifer as she thought that they could probably be good friends.

"Sure, go ahead, I'll be just outside of the door if you need me."

Once the Doctor had left, she sat down next to John and held his hand feeling surprised at how cold it felt. She was about to ask Dr Keller about it until she realised that the doctor had left the room.

She turned back to John and started to speak to him softly hoping that he might hear her.

OOOOOOOOOOOOOOOO

John moaned as he slowly became aware of the sounds around him. The jackhammer was still redecorating his skull and there was something itchy under his nose. He heard soft voices beside him, and he was positive that one of them was his mother and the other one was his brother Dave.

His brain was still muddled as he tried to open his eyes, he was sure that he should be on Atlantis, his mother was dead and he and Dave hadn't spoken in years, but if that was true then why were they here.

When he finally managed to open his eyes, he was disconcerted to find that he was still blind.

"Teyla," he whispered, hoping that he was in the infirmary on Atlantis.

"No, John it's Dave and Mom is here with us too."

"What happened, why am I not in Atlantis?" He asked them still feeling totally confused.

His mother spoke to him in a soft gentle tone "You were in a chopper crash John, don't you remember?"

Slowly everything was becoming clear to him, he was infected by nanites and this wasn't real, and he was positive of it, the only problem was as his mind became clearer the pain in his body began to notch up again.

"Yeah, I vaguely remember it, how long have I been here?"

"You've been here for around four weeks," Dave answered in a surprisingly gentle tone.

The last time he remembered waking up he'd only been there for three weeks, so he'd been unconscious in this fake reality for another week. That's if time flowed at the same rate as the real world.

He knew that without his sight it was going to be exceedingly difficult to find a way out of this mess, so he had to try and find out as much information as possible, "why can't I see?"

"You received a brain injury in the crash. Dr O'Neill is certain that your eyesight will return eventually, but he has no idea how long it will be." Dave answered him.

"This isn't real, I have to get back to Atlantis," John stated trying to get out of the bed, despite the pain he was in.

"John please lie down; Dave has just gone to get Dr O'Neill as he wanted to know when you were awake again."

He very quickly acquiesced to her requests and was relieved when she started to whisper to him while wiping a soft cloth over his forehead. He tried to picture her face and all he could come up with was an image from when he was thirteen years old before she had become sick. Her hair had been as black as the darkest night, her eyes were a deep hazel just like his, her skin was alabaster and to him, she was the kindest and most caring person that anyone could ever meet.

The last time he saw her was almost twenty-five years ago, so if she'd still been alive now, she'd be in her mid-sixties.

Before he had a chance to contemplate what she may look like now a voice he'd never heard before interrupted his thoughts.

"Major Sheppard, it is good to see you awake. My name is Dr Fletcher, and I am the hospital psychologist."

Suddenly he found himself tumbling into a swirling dark pit and it wasn't long before he lost consciousness again.

OOOOOOOOOOOOOOOO

Elizabeth entered the infirmary to find Carson sitting with John and whispering in his ear. She'd spent all morning in her office catching up on paperwork and she desperately needed a break. John had been unconscious for two days now and he showed no signs of waking. She or a doctor or a member of John's team had been with him at all times.

"How is he Carson, is there any change?"

"No, he's not getting any better, but then he's not getting any worse either."

"He's been unconscious for two days, Carson, how long do you think it will be until he wakes up?"

"I don't know lassie, it could be five minutes from now, or it could be five days. The only piece of good news I can give you is that he's just unconscious and not in a coma."

"Do you mind if I sit with him for a while?"

"Sure, go ahead lassie, I was just going to get something to eat. Dr Keller is in the office if you need anything."

"Thanks, Carson."

She stood and watched him leave, then she sat down next to John and held his hand. To her surprise, it was much warmer than it had been two days ago after the accident in his quarters.

Settling back in the chair she started to talk to John and tell him about her day. After twenty minutes of talking, he still hadn't shown any sign that he knew she was there so she decided that she would go and get a cup of coffee and come back later.

Just as she was about to stand up and leave the room a moan came from the bed and when she looked down, she saw the most wonderful sight she'd ever seen a pair of hazel eyes were staring up at her.

OOOOOOOOOOOOOOOO

When John awoke again, he found that he was still tumbling in the swirling darkness and he wondered if the pit he was falling into had a bottom. He heard soft voices in the distance and shuddered when he thought of where he'd been the last few times he'd awoken. He moaned as he continued to fall through the inky blackness. There was only one voice now and it was a voice that he recognised the only problem was he couldn't put a face to it, was it his mothers, or perhaps it was Elizabeth's, he didn't know for sure, so he struggled to try and open his eyes. The pain in his head intensified and he hissed as he felt pressure in his head, but he knew that he needed to wake up and let Carson and Elizabeth know that he was infected by nanites, so he tried to open his eyes again. After three unsuccessful attempts, he finally managed the feat and was devastated when everything was still dark.

"Elizabeth is that you?" He whispered.

"It's good to see you awake John, would you like a drink of water?"

He began to panic, he was blind and infected by nanites so the last thing he needed was to chat with Elizabeth and have a drink of water, "Elizabeth I really need to talk to Carson now!?" He stated as forcefully as he could, given the pain he was in.

"Are you alright John?" She asked and he could hear the confusion and worry in her voice.

Gritting his teeth, he reached out and tried to grab her arm, but being blind he missed it. She must have sensed what he was trying to do so she held his hand.

"Elizabeth I can't see, and I'm infected by nanites so can you please get Carson for me now?" He practically begged her.

He heard footsteps as she turned and walked out of the room, so he closed his eyes and laid back against his pillows. He really hoped that he could stay in the real world for a while, even though his mother was alive in the fake world.

It wasn't long before he heard footsteps again, which didn't do anything for his throbbing skull, and it was made even worse when Carson spoke a little too loudly a second later.

"How are you feeling Laddie?"

"Please keep the volume down doc, and the answer to your question is I have a pounding headache, I can't see, and I'm infected by nanites."

"I've done five tests now and they have all come back negative for nanites, so why would you say that?" Carson asked in a much quieter tone.

He knew that Elizabeth had re-entered the room with Carson because he could smell her perfume, so he turned his head in the direction where he thought she was and spoke to her, "because I've just had a visit from the good Dr Fletcher."

The pain in his head was intensifying again, the tiny white-hot needles were digging into his brain again and he could feel his grip on reality slipping again. He knew that he didn't have long before he was ripped away from the real world and plunged into the swirling darkness. The last thing he heard before he slipped into unconsciousness again was a gasp from Elizabeth.

TBC…