Disclaimer: Stargate Atlantis - and all the characters and settings related to the show - do not belong to me, obviously. That credit goes to MGM, Brad Wright and Robert C. Cooper. The plot of this little story, however, does.

A/N – Hello again! Sorry for the slight delay in posting this chapter – it's been a busy week, and unfortunately I just haven't been able to find any time to write until now. This chapter isn't the longest one I've ever written either (although it is the longest chapter in this story so far) but it includes plenty of hurt!John and angst from pretty much everyone involved, so I hope you'll like it anyway - enjoy!

~ Alone ~

Part Three

When the next morning finally arrived, bright, crisp and cold, John woke slowly.

At first, he wasn't even really aware that he was waking up. On some level he knew – or at least he felt alive, but for those first few seconds his mind was so clouded by pain that he could barely comprehend anything beyond the simple fact that the darkness in his head was beginning to lift.

Eventually, after what felt like an age to John, his mind began to register other things as well. The beating of his heart; a little too fast, but beating nonetheless. The air being pulled into his lungs by instinct alone, keeping his body working while his mind fought to catch up. The white hot pain on the side of his temple, pulsing so intensely that it pushed all other aches and pains into the dark recesses of his clouded mind.

After a few more moments – and a few silent but heartfelt curse words – John was able to get control over the pain as well, finally allowing his mind the freedom to focus a little less on his own battered condition, and a little more on his immediate surroundings. With a bit of concentration, John could feel hard metal below his shivering body. He couldn't hear much going on around him, but the freezing cold chill in the air around him, as well as the soft breeze rustling in his dark hair, suggested that he was either outside or, if he was inside, that someone had left the door wide open to the elements.

Where was he…?

John felt hungover - wrung out, nauseous, and with a hell of a banging headache - even though he knew there was almost no chance that he was. As the remnants of sleep finally began to leave him, achingly slowly but surely, John was able to focus a little more, drawing on every little bit of training he'd ever had in order to try and work out what was going on.

God, what the hell had happened to him?

Well, there was only one way to find out, he supposed. John groaned, and finally dragged his eyes open. The sunlight hit him hard at first, but he blinked hard and eventually his vision adjusted.

To say that he was surprised to find himself in a jumper was an understatement. The fact that he was lying down on the cold, hard floor of said jumper was actually less of a surprise. It definitely explained why he was so uncomfortable, and why his body was aching from top to bottom. Now that he thought about it, John did have a vague memory of collapsing on the floor of the jumper late the night before, although he wasn't really sure why he had…

What the hell had happened?

This time, as he glanced around the empty jumper from his position on the floor, John forced his mind to remember, focusing all his energy on bringing the elusive memories back to the forefront of his mind. He knew it would no doubt be painful – both figuratively and literally – but he'd always been the type of person who just had to know. And this time was no different, not least because he was quite clearly hurt. For all he knew, he could still be in danger…

Please don't do this…

With a wave of nausea that almost made him lose the little that was left in his stomach, the memories seemed to hit him all at once. John pulled himself upright with a desperation even he didn't fully understand, but immediately regretted the sudden movement when his vision flashed bright white and the stabbing pain in his right temple returned with a vengeance.

John groaned, but kept his body upright by sheer will alone, rubbing tiredly at his face in an attempt to keep himself conscious. He wouldn't be able to stand up any time soon, but even sitting upright was a victory he sorely needed. The truth was he ached all over, and even though the inside of the jumper was dry and relatively protected from the cold wind outside – despite the hatch door being left wide open- he couldn't stop the shivers that were wracking his body. Which, he realised, probably wasn't a good sign…

Please don't do this…

The memories were back now, and John could do nothing to get rid of them. He remembered it all.

He remembered being marooned on a planet light-years from Atlantis. He remembered his friends punching him, kicking him, telling him that he deserved it. That he wouldn't be missed…

He remembered them leaving him behind, alone, and he remembered the gate and DHD blowing up not long after they had. After that, his memories were a bit blurry, which he had a sinking feeling had everything to do with the concussion-like symptoms he was experiencing at the moment.

John shook his head as he tried to pull himself together, steadying his rapid breathing as best he could. He couldn't afford to panic, not if he was going to survive this. Not if he was going to make it home…

With a force that called on all of his reserves, John focused his mind again, fiercely ignoring how much it hurt. He had a vague recollection of pulling himself free from the ropes that Ronan had used to tie him to the tree, and he remembered staggering away from the tree towards the dead jumper. He must've blacked out at that point though, because the next thing he remembered was falling into the pilot's seat in a desperate attempt to see if it could fly.

Of course it hadn't, and then John remembered trying to see what supplies he had instead, though he couldn't recall now if he'd been meaning to fix the ship, or if he'd just been focused on surviving a little bit longer. Either way, he must've blacked out again, because definitely hadn't made much headway on even that small task. He'd managed to find the medical supplies, that much he did know, but he could only remember picking up the first aid bag, not actually using any of the supplies in it. Which would certainly explain why his head was pounding and still felt wet to the touch. Blood, and plenty of it, which definitely wasn't good…

John groaned again and tried to stop the room from spinning. He needed to get up. In this type of situation, the first few hours were crucial, and he'd spent his unconscious on the floor of the dead jumper. He needed the get the lay of the land, and figure out what he had to work with in terms of survival supplies.

Please don't do this…

John shook his head and forced the memory away. The only way he was going to survive would be to focus only on survival. Anything else would distract him, maybe even break him...

John took a shaky breath as he pulled himself to his feet.

He would get through this, he told himself. One way or another, he would survive.

Dr Carson Beckett was silent as he watched the rising chests of his three newest slumbering patients. The Infirmary itself was quiet as well, save for the steady beeping of the machine measuring the three separate heart-rates. It was early in the morning, and most of Atlantis hadn't woken up yet. Of course, as always, there were some that had barely had any sleep at all…

"So, what are your thoughts, Doctors?" Woolsey asked quietly as he looked down at the unconscious and unmoving forms of Ronan, Teyla and Rodney.

Carson sighed deeply, and shared a glance with Jennifer Keller as he tried to find the words to explain what he didn't even really understand himself. His mind and body were both exhausted, having been up all night trying to get to solve the mystery of what had happened to Atlantis' premier team, but he still felt no closer to an answer.

All they knew at the moment was that upon arriving on Atlantis, notably minus their team leader, Ronan, Teyla and Rodney had promptly collapsed. Woolsey hadn't even been able to get one word out before each of them had dropped to the floor like puppets that'd had their strings cut. It had been unnerving to witness, to say the least...

In the hours that had followed, and despite the best combined efforts of Beckett and Keller, the three members of SGA1 hadn't woken since, although their vitals had at least remained reassuringly steady. The downside, of course, was that the doctors still had no idea what the hell had happened to them, and even worse, they had no way of finding out where Colonel Sheppard was, or whether he was even okay…

"Doctor?" prompted Woolsey.

"Well, they're alive," Beckett replied finally, running a hand over his tired face. "I'm afraid we don't know much more than that right now."

"When do you think they'll wake?" Woolsey asked.

"It could be any time, or not at all," Jennifer replied, her eyes fixed on Rodney in particular. "We really have no way of knowing. They're not in a coma, I can tell you that much, but they're not experiencing normal REM sleep either. We simply don't know what caused this, and nothing we've tried has had any effect so far. We're not giving up, but until we get more information, I'm afraid it's up to them."

"I realise you're working blind doctor, but I can't in all good conscience allow anyone back to that planet until we know what happened, and how to stop it from happening again," Woolsey said heavily. "I just wish there was more we could do to find Colonel Sheppard..."

It was a Catch 22 situation, but it was something Beckett knew couldn't be helped. Woolsey, as leader of the expedition, had to think of the bigger picture. The Scot couldn't help but think of Colonel Sheppard though. Beckett knew that Ronan, Teyla and even Rodney would never have left John behind. Not willingly….

"Colonel Sheppard is a strong man," Beckett told Woolsey and Keller, almost trying to convince himself as much as them. "He'll find a way to survive, he always does. We'll get him back."

"If he isn't already…" Woolsey trailed off, unwilling, it seemed, to even finish the dreadful thought.

"There's not much point in speculating at the moment," Jennifer interjected. "We need more information, and until we get some, we have to work off the assumption that Colonel Sheppard is alive. Like Carson said, we'll get him back. And in the meantime, we have three people right here to look after."

"Okay," Woolsey said with a sigh. "Well, keep me updated on their condition. If – no when they wake up, I want to be the first to know."

"Of course," Beckett said. Then he turned to Jennifer. "I can stay and keep an eye on things for a while if you want to go and get some rest."

"I suppose I should," she replied, although she seemed reluctant to even admit that much. "I don't want to leave, but I have a feeling I'll be needing the energy sooner rather than later."

"Aye," Beckett agreed, glancing down at the slumbering team-mates. "I reckon we all will."

John sighed deeply as he scratched roughly at the stubble on his jaw. When he'd first woken up, he'd been more worried by how much time he'd lost than anything else – particularly since his watch was useless on a planet that almost certainly didn't follow Atlantis time – however judging by the length of the stubble on his jaw, something that was growing itchier by the minute, he'd only lost one day at the most.

Which was one more than he would've liked, obviously, but certainly less than he'd feared at first.

John swallowed back the nausea and dizziness that were still plaguing him, and instead focused on putting one foot in front of the other. He was determined to walk at least the perimeter of the clearing and check out what the surrounding area had to offer before he allowed himself to rest. If this was to be his home, he had to make the most of it.

Despite his doubts, John knew deep down that Atlantis would be looking for him, and if he knew his people - and he did - then it was a safe bet that they would eventually find him. He just had to hold out long enough for them to find him alive.

John had undergone extensive survival training since he'd joined the Airforce, so he knew what he was doing. The fact that this was an unknown planet didn't matter. All he needed was a water source, a sustainable food source, some form of shelter, and something to offer protection against any predators in the immediate vicinity. The latter was already proving the most difficult, particularly as his team hadn't left him with any guns. He'd managed to find two hunting knives, but how much protection they'd offer against any potential attackers remaining to be seen.

God, he really hoped there weren't any attackers…

John shook his head and focused back his internal survival check-list. The rest of them were proving a little easier to sort out. It helped that he already had shelter in the form of the dead jumper. He'd tried everything he could think of to get it moving, but he'd not had any luck so far. But even though it was dead, it was sturdy and waterproof, and sleeping on the floor of the jumper definitely beat sleeping out in the open. It wasn't perfect – especially since he hadn't been able to get the hatch door to close– but it would do, and one big bonus that came from having the jumper was that the jumper contained plenty of supplies – medical as well as food and drink.

The food and water probably wouldn't last very long since they hadn't packed for a long mission, but it would be enough to him the chance to recover physically before he would be forced to go searching for a fresh water source or hunting for food.

John shivered, and pulled his jacket more closely around his body in an attempt to keep warm. He knew he would need to start a fire when he got back to the jumper, so he made a point to collect the driest leaves and twigs he could find as he continued to make his way around the clearing. He hadn't been able to shake the chills which had been wracking his body for the couple of hours, and he knew from experience that his condition would only deteriorate if he didn't address it soon. The fact that he was still dressed in slightly damp clothes probably wasn't helping, but since he didn't have any other clothes to change into at the moment - not even a spare jacket - he didn't really have a choice. Once he got the fire going, he change out of them for a bit and try to dry them off. Hopefully then he'd start feeling a bit better…

John swallowed back his nausea, as he stumbled slightly. On top of the chills – and his generally battered condition - he knew he probably had a concussion. Generally speaking, the advice would be that he should rest – something he again knew from experience - but since he was alone, he simply didn't have any choice but to keep going. He had to do this now, because if he didn't, he sure as hell wouldn't live long enough to do it later.

Please don't do this…

Damn them for leaving him behind, John thought suddenly, clenching his fists as he rode the first wave of anger. His friends had done this to him, intentionally or not, and he hated it. He hated being the one who always got left behind. What was it about his personality that made people do this to him?

John knew he wasn't being fair, but he felt sick, the pain in his head was spiking, and his body felt exhausted beyond all comprehension. He could barely put one foot in front of the other, but he knew it would be a while before he'd be in any position to recover properly. Sighing deeply, he began to make his way slowly back to the jumper.

Survive. He just had to survive. Thinking about his friends wasn't helping. He was only into day two of his exile, and already he was falling apart. He had to get a grip on himself and forget about them. It was the only way he was going to get through this.

Survive, he told himself, almost like a mantra. He just had to survive.

Back on Atlantis, the hours were passing slowly. It felt a little like they were in limbo - frozen in time, waiting for something to happen, but dreading it at the same time.

Of course, Beckett - who had now been awake for 25 hours and counting - was so exhausted by the act of waiting for something to happen, that he almost missed it when it did.

It started with a change in the beeping heart-rate monitor. It wasn't all that unusual for unconscious patients' heartrates to fluctuate, so Beckett dismissed it at first. What he couldn't dismiss, however, was when Rodney's hand began clench, and his eyelids began to twitch.

Beckett was at Rodney's side in seconds, heart racing in anticipation.

"Rodney," he said softly. "Can you hear me? You're in the infirmary."

Keeping his eyes fixed on Rodney, Beckett signalled to the soldier he knew was standing on duty by the door. He had a feeling he was going to need back up.

"Come on, Rodney," Beckett encouraged. "That's it. Time to wake up."

Rodney's eyes flickered again. This time his other hand started to twitch as well, and he moved his head slightly to the side. Beckett held his breath, then released it slowly in an attempt to calm down his racing heart.

"Come on, Rodney - "

"Carson," Rodney mumbled, eyes still firmly closed. "Shut up."

The doctor's relief was palpable. Beckett could feel it in his bones, and he almost sagged with the strength of the feeling that had hit him in that moment.

"I can't, I'm afraid," Beckett continued, pulling himself together long enough to do his job. "You need to wake up."

"Don't want to," Rodney replied, stubbornly keeping his eyes closed. "Head hurts."

"I'm sure it does," Beckett replied, "But Rodney we need your help."

That seemed to get through to the stubborn scientist, and this time Rodney cracked his eyes open. "What happened?"

"Actually, we were hoping you could tell us."

"No idea," Rodney replied, grimacing slightly.

Carson watched in silence as Rodney pulled up his head slightly and took in his surroundings, his gaze landing on Ronan and Teyla, both of whom were still unconscious. The scientist nodded towards them. "They okay?"

"We're not really sure," Beckett replied, relaxing slightly when he realised his backup had finally arrived in the form of three burly marines. About time. He turned his attention back to Rodney. "How do you feel?"

"Head hurts," Rodney repeated, shooting him a disdainful look. Beckett bit back his own sharp reply, recognising that it was neither the time nor the place for their usual bickering.

"Anything else?" Beckett replied patiently, settling for a roll of his eyes instead.

Rodney, however, was no longer listening. Instead, he was looking around at the other occupants of the infirmary, a frown on his face as his gaze fell on Teyla first, then Ronan, and then finally the empty bed beside them. Beckett could almost pinpoint the moment that the scientist put two and two together.

"Carson?"

"Yes, Rodney?" Beckett replied with a sigh.

"Where's Sheppard?"

A/N – Dun, dun, dunnn! So, Rodney doesn't remember what happened to Sheppard - that, I'm afraid, is going to make thing a little more difficult for the rescue team! Of course, John isn't going to have it easy either (quite the opposite actually), but I won't say anything more now since I don't want to spoil it for you all! In fact, I'll just leave it at this - I hope everyone's still in character, and that you liked this chapter. If you did, I'd really appreciate it if you could take a minute to give me your thoughts. Otherwise, and until next time, thanks for reading!