John awoke to the sound of tapping keys; he could feel a warm body beside him and was momentarily worried that he might be waking up next to Rodney.

Usually, when he woke to that sort of intermittent clicking, he was in the infirmary, Rodney at his bedside, typing away and oblivious to the world around him.

He cracked his eyes open and looked over to see that Elizabeth was sitting up in bed and writing up reports, laptop resting on the covers, her lips pursed and a frown creasing her features.

"Hey," he said yawning and rolling his aching shoulder.

"Hey," Elizabeth said shooting him a quick look.

"You didn't wake me, what time is it?"

"A little after eight," she said as she continued to type.

"And you didn't wake me?" he asked again as he sat up in bed.

"I thought you could do with the rest," she said.

"We should be up," he said as he checked his watch.

"No, I should be up. You should be resting."
"Why aren't you up?" he asked placing his hand on her leg.

"Did I mention you've been in a coma for two weeks?" she flashed him a smile, "I wanted to spend a little time with you."

He smiled back, "I feel like we're truanting."

"I am," Elizabeth said as she closed her laptop, "I'll get up in a bit."

"Aren't you worried somebody might see me leaving your quarters?" he asked waggling his eyebrows.

She gave him a playful poke, "This is the first time in weeks that I've had a lie in and no, I'm not worried."

"Okay," John said as he lay back down.

Elizabeth placed her laptop on the side table and snuggled up beside him.

"I'm sorry about last night. You mad?"

"Well at least you didn't hit him," she said as she ran a hand along his chest, "I'm just sorry it happened."

"Simon's an ass," John muttered.

"Simon came here for the wrong reasons," Elizabeth said, "And he'll be leaving soon, as you said."

"So, when am I getting back on duty?" John asked as he ran a hand through her tousled hair.

"John," she warned.

"Come on, going out with the head of the expedition should give me some perks."

"You're getting the perks Colonel Sheppard," she chided, "You'll return to duty when Carson says so."

She leant up on her elbow and gave him a kiss, his hands found her chin and he gave it a stroke as she broke away, "I'm on light duty," he said pulling away, "I can't do anything strenuous." He joked.

She smiled and kissed him again, "Kissing me isn't classified as strenuous."

"I don't know," he said with a grin, "Carson has spies."

Elizabeth batted his arm lightly, "Fine." She pushed the covers aside and got out of bed and headed for the shower, "I'll just shower on my own then," she said as she tossed him her t-shirt.

John lay in bed, heard the shower start up and then groaned, "You'll be the death of me Doctor Weir," he muttered before getting up and following her.

--------------------------------

The conference room was filled with a tension that Rodney was oblivious too as he spoke.

John was sitting beside Elizabeth, Simon on the other side seated next to Carson, and next to them was Teyla.

John kept looking over at Simon, and Simon kept avoiding his gaze. All the while Elizabeth was giving John looks to communicate to him to stop it. John gave her a "What?" look and then smirked.

"So, they've all been relocated, they're doing remarkably well and my cure seems to have worked," Rodney said as he folded his arms.

"Simon's cure," Carson added with a heavy sigh.

"Hey," Rodney griped, "I was instrumental in their recovery. If it hadn't been for my-"

"Whining," Carson said.

"Allergies," Rodney stated, "You would never have realised that it was the cure."

John had been listening to them for the past half hour and felt well and truly out of the loop. He was not used to hearing information after an event, usually he was the one battling to help find a cure, or just plain help in some way.

Sitting at the head of the table, the talk of the ill and the cure, he knew he was just another one of the cured casualties and had very little to add.

"Did you go back to their village?" John asked.

"It was destroyed," Teyla added mournfully.

"What about the coma patients back there? We had to leave them," John admitted sadly.

"Aye, they were dead," Carson said with a note of sadness himself.

"We should have helped them," Simon blurted out suddenly and all eyes were fixated on him.

John sat forward in his chair, mindful of his bad shoulder, and looked Simon in the eye, "Its unfortunate, but we can't save everybody. We barely made it out of there ourselves."

Simon continued regardless, "We could have helped them somehow. Hid them, transported them to a more secure room or-"

"No," Johns stated firmly, "If we'd had time we could have, but we didn't."

"If you hadn't got shot-"

"What has that got to do with it?"

"You wouldn't have been indisposed and we could have hel-"

"Gentlemen," Elizabeth said suddenly.

She was aware that everyone was looking at her. Knowing that she and Simon had once been together and feeling uncomfortable because of it.

"It sounds as if there was nothing more that you and John could have done."

"You would say that," Simon said.

"What do you mean?" Teyla asked, interested.

John and Elizabeth shared a quick look.

Simon shook his head, "Nothing."

Teyla looked around the table, a puzzled expression on her face.

"Do we have anything else to discuss?" Elizabeth asked as she leafed through the folder in front of her.

"There's an address I'd like to check out soon," said Rodney, "From the database."

Elizabeth indicated for him to continue.

-----------------------------------------

The conference went on longer than expected and once it had ended John and Elizabeth went out to their favourite balcony for a breather.

They had both just leant against the railing when the door slid open and Simon walked out to join them.

"What's he doing here?" John whispered to Elizabeth. "Simon?" he said turning and leaning against the railing.

Elizabeth turned to Simon and crossed her arms over her chest. "That was unprofessional behaviour in the briefing." She flinched even as she said it because she knew what Simon would say.

"You're talking to me about unprofessional conduct?" he asked as he stood in front of them, "Did your boyfriend tell me he came to see me last night?"

John licked his lips and looked down at the floor guiltily.

"I've spoken to John about that," Elizabeth provided, "And he's sorry."

John turned to her, "I am?" Like hell I am.

"Yes, he is."

"Elizabeth," said John leaning in to whisper to her, "He tried to-"

"I know," Elizabeth said stepping away from the balcony and raising her hands, "He tried to kiss me. I'm just sick of this…" she said with a sigh.

Simon looked guilty as hell as he said, "I am sorry that my feelings ran away with me. I crossed a well established line."

"I was in a coma," John said in a low voice. He was trying to keep his anger in check, trying to remain cool.

"I know," Simon said, "I just……." Words failed him and he ran a hand through his hair.

"Simon," Elizabeth walked over to him, "I'm happy." She turned back to John to see him looking away from them, "Can't you see that?"

John cleared his throat, "Maybe I should leave, so you two can…..talk," he said.

He strode over to the door, expecting it to slide open for him, and was surprised when he walked straight into it. He staggered backwards, cupping his nose and cursing, and turned back to Elizabeth, "What the hell?"

Elizabeth tore her eyes away from Simon and walked over to the door.

It didn't budge.

"Control, this is Doctor Weir. We're having an issue with the balcony door leading into the control room." There was a moment of static through the earpiece and then the gate technician's voice came through.

"We've started to get reports all over the city." There was a brief pause, "The city has gone into lockdown."

John tapped his earpiece and joined the conversation, "Lockdown?"

"There doesn't appear to be a reason for it. We're working on it."

"Patch me through to Doctor Mckay," John instructed.

He walked over to the balcony and Elizabeth listened as he began to talk to Rodney.

She turned her attention back to the technician, "You're sure that there is no immediate threat? No contagion?"

"None."

"Okay, well, keep me updated."

Elizabeth glanced over at John, who was gesticulating wildly as he spoke to Rodney, and then joined Simon.

"What's going on?" he asked as he looked over her shoulder towards John.

"The city has gone into a lockdown," she stated.

"Looks like we're going to be here for a while," John shouted over to them, "Rodney says its related to the power spikes they've been having and he thinks something has shorted out…." He narrowed his eyes and then sighed, "Rodney, I know its not that simple…well, yes………but…..Rodney." He turned his back to them and leant against the railing to continue his talks.

Elizabeth and Simon walked over to the wall and sat down beside one another.

"Should we be worried?" Simon asked as he pulled his legs up to his chest.

"If Rodney says it's nothing to worry about then I believe him," she wrapped her own arms around her legs, "We'll just have to sit and wait this one out."

"You said…that it could be a contagion?" he looked over at her and averted her eyes when she met his.

"Rodney has been investigating the problem. When we had the incident with the bugs here, the city should have detected that there was a problem and gone into lockdown. It didn't. He thought that maybe the bugs responsible were so minute that the city couldn't detect it…but he has his suspicions that there might be a bigger problem."

"Oh," Simon muttered, "Has this sort of thing happened before?"

"We had a nanovirus last year, the city closed itself off to contain the sick…" she looked over at John. He was still pacing back and forth and talking loudly, "I almost lost him then," she stated quietly.

"Lost him?"

Elizabeth took in a deep breath and then met Simon's eyes, "The only way to disable the virus was to expose it to nuclear radiation. John took a nuclear device into the atmosphere and detonated it, he saved everyone's lives, but we thought he'd been killed in the explosion." She sighed heavily.

"Sounds……" Simon fought to think for the right word, "Idiotic."

Elizabeth chuckled.

"I still don't think he's any good for you," he said reaching out and squeezing her arm affectionately, "And I say that because I really do care for you."

"Simon, he makes me happy."

"But he's reckless."

"He's not reckless. He's passionate. I remember that's why I first fell for you."

"Yeah?" Simon smiled fondly at the memory of their first meeting, "He'll die out here. You'll be left on your own."

"We've had this discussion, John and I, we're aware of the risks."

A comfortable silence settled between them and Simon finally broke it.

"I'm sorry that I tried to kiss you."

Elizabeth turned to him, "I'm not going to ask you to stay. I think you came here for the wrong reasons. I really want to give my relationship with John a fighting stance."

"You're keeping it a secret."

"Not because we want to, because we have to."

"Okay," Simon said sadly.

"I'm going to see what's going on," Elizabeth said.

She stood up slowly, and gave him another look before walking off, "You'll always be important to me Simon, but it's time to move on."

Simon looked down at his feet and didn't look up.

It was only when he heard Elizabeth and Sheppard talking did Simon look up.

Sheppard was smiling as he spoke to her, his eyes focused purely on her, his hand resting on the small of her back as he guided her over to the railing to talk.

Elizabeth was looking back at him with the same intensity. He remembered when she used to look at him like that and felt his gut twist.

He listened as their voices floated towards him.

They continued to talk in hushed tones and after a few minutes, Elizabeth touched her earpiece and began to talk, presumably, to Doctor Mckay and Sheppard came to stand beside him.

"So, it looks like we're going to be stuck here for a while," said John as he began to pace back and forth, hands hooked in his belt loop.

"I presume Doctor Mckay is working on the problem," Simon stated as he watched Sheppard's feet.

"Well, Rodney's got stuck in one of the transporters and he's claustrophobic. He's got his data pad and he can bring up the schematics on the screen in there," John continued to pace, "But yeah, he's working in it." He stretched lazily, grimacing when it pulled on his shoulder.

"If it's going to be a long wait, maybe you should sit down."

"I'm fine walking around."

Simon sighed, "You'll wear a hole in the floor."

In truth, John was feeling tired and shaky and should really be in bed resting.

After a few minutes, he didn't have the energy to be stubborn, and he sat down next to Simon, spreading his legs out and dropping his hands down into his lap, "I'm really hungry," he muttered and reflexively checked his pockets just in case he had a stray power bar. He didn't.

Silence descended between them. It was always uncomfortable and needlessly protracted.

"It looks like you've won," Simon finally said.

"What?"

"I'm leaving; you'll have Elizabeth to yourself. You've won."

John went to get up. He was tired of having this conversation with Simon.

"No, don't…" Simon sighed, "Sit. I didn't mean to…" he paused and shook his head, "It's over between us. I get that now."

John settled back again and turned to Simon, unsure of how to respond.

"Just make sure you don't hurt her." It was acceptance and it was strange hearing it from Simon.

"I'll never hurt her," John stated.

"She told me you went on a suicide run."

John looked over to Elizabeth. She was leaning against the railing, still talking to Rodney. "Well," John said licking his lips, "We were under attack from the wraith. It was our last chance so I took a nuclear device up to a Hive ship to deton-"

"Wait," Simon turned to him and held up a finger, "I thought it was a nanovirus?"

John closed his eyes and then said quietly, "Well, that was a ……different occasion." He bit his lip, "The nanovirus was before-"

"So you went on a suicide run…..twice?" Simon asked with a disbelieving look.

"Yeah."

"Oh."

"But that was before……and….." he sighed, weariness pervading his every thought process, "I did what I had to do. And it was to protect Atlantis. Elizabeth."

Simon retreated into himself, silence veiling them again, the sounds of the sea below their only comfort.

"If I had to do it again to save her. I would."

"You'll end up hurting her," Simon admonished.

"Everything is different here," John said crossing his legs to get into a more comfortable position, "Its dangerous here."

"Fine," Simon held his hands up, "I'm sorry. I don't understand. You both seem to have this…worked out."

"We don't have this worked out. Its trial and error, "John admitted, "But, I do care for her. You know I do so you have to know that I would never do anything to hurt her."

"You wouldn't cheat on her?" Simon asked as he picked at some stray material on his pants.

"Absolutely not."

"You wouldn't leave her, intentionally?"

"No."

"She's very special," Simon said as he glanced over at Elizabeth, "She likes to think that she's strong, but she isn't. She's fragile."

"I know what she's like."

"I mean it," Simon interrupted him, "I was with her for five years and I know how she thinks. She's a born worrier."

"I'm not going to hurt her Simon."

"Because if you do…I'll be straight back here." Simon knew it sounded ridiculous, but he wanted the threat to be there. He needed Sheppard to understand.

John looked over at Elizabeth and then turned to Simon, keeping his voice low and even, "I love her Simon…and I've never loved anyone."

"Have you told her that?"

"Not in so many words."

Simon looked down at the floor, his eyes unwillingly straying back towards Elizabeth, "Just make her happy."

"I will."

"Good."

"Great."

The wind was picking up, there was a chill in the air and John looked up to the horizon, "Damn."

"What?" Simon asked hugging himself to keep warm.

"See that?"

Simon could see the rolling black cloud that seemed to be getting closer, "Rain."

"Rain," John repeated.

"I hate rain," Simon muttered and he looked up to see that they had little cover.

"If I get so much as a cold, Carson is going to kill me."

"Well, you shouldn't be up and about. You should be resting."

John sighed and shot Simon an irritated look, "I would have been if I wasn't trapped here."

"Well, you certainly shouldn't have been in that briefing."

"It was Intel I needed to know," John defended tucking his hands under his armpits.

"You lost a lot of blood, your muscles are still weak from the coma-"

"I felt fine this morning," John said even as he felt his eyelids dropping closed. A gust of icy wind had him snapping them back open, "Could you just not nag me for one minute?"

"I'm not nagging."

"Yeah, right," John muttered under his breath.

John watched as Elizabeth turned, shot him a smile and then returned to her talks, her mouth moving and tinged with a wry grin.

"What are you going to do when you return to earth?" John asked. He hated the silence and felt the need to fill it. There was a strange tension between them that even Simon accepting their relationship could not break down.

"Return to the Hospital, continue my residency there. They gave me the option to return."

"And Sedge…was it?"

"Get him back off my brother. Find myself somewhere to live," he shrugged, "I'll figure something out."

"I'm sure you will," John said at a loss for anything else to say.

"What's going to happen here?" Simon asked apprehensively.

"We're still at war with the wraith. I'm still searching for Ford. Life will go on."

"And still be dangerous."

"And still be dangerous."

"Don't you ever get tired of this?" Simon asked wearily, "I've only been here a few months and that one trip off-world was enough to scare the hell out of me."

"I'm used to this," said John.

"Was that off-world trip…standard?"

"Pretty much." It was Johns turn to shrug, "You get surprisingly used to it."

Elizabeth finally deactivated her radio and came to sit opposite the two men, pulling her legs up to her chest, "Rodney says he'll get in contact when he knows more."

"He still panicking?" John asked with a grin curving his lips.

"He's in a wide open field," Elizabeth said mirroring his smile, "He's got Zelenka helping out."

"So, still stuck." Simon stated.

"Yes and…" Elizabeth said hooking a thumb behind her, "It looks like its going to rain."

"Should have worn my jacket," said John, noting that both she and Simon were wearing theres.

"You shouldn't even be out here. You should be in bed resting." Elizabeth remarked.

John rolled his eyes and smiled, "I know."

----------------------------------

Two and half hours had passed and the rain cloud had got much closer, the weather had turned for the worst, the wind had picked up and the air was chilly.

Their conversations had been forced, disjointed and uncomfortable.

"Eye spy with my little eye, something beginning with W," John stated as he rubbed his forearms.

"Water," Elizabeth and Simon said simultaneously.

"Surely Rodney should have figured this out by now?"

"He's wo-"

"Working on it," John said with a nod, "I know. I just wish I hadn't skipped breakfast."

"You skipped breakfast?" Simon said with an incredulous tone.

"I was preoccupied this morning," John said as he flashed Elizabeth a look.

She flushed red and looked down at the floor and John noticed that Simon didn't miss their looks. If he could have, Simon would have probably vomited there and then.

There was a rumble above them and the sky flashed white.

"Okay," said John, "Here it-" He didn't finish the sentence because the skies opened and the rain began to fall.

They all scrambled to their feet and pressed themselves up against the wall as the rain fell in sheets.

"Okay," John shouted over the rain, "Rodney had better hurry up."

Elizabeth's hair was beginning to get plastered to her forehead as the rain fell at them sideways. She felt a warm arm fall around her shoulder and John pulled her close.

"Well, I don't think things could get any worse," Simon shouted.

"Tell me you didn't say that?" Elizabeth remarked.

"What?" Simon shouted back.

"We don't ever say that!" John informed him, "Bad luck."

"How could we have more bad luck?"

John was about to respond when he heard his earpiece crackle and Rodney's voice came across the airwaves. "Tell me you've got this figured out? I'm freezing my ass off out here."

Elizabeth and Simon shared looks as John continued to talk, the other half of the conversation unheard to them.

"Okay, okay. Keep us in the loop," he switched off his radio, "He's going to reboot the city."

"What?" Elizabeth asked as she licked the rain off her lips.

A crack of thunder above them forced them all to look up.

"He's going to get someone to take the ZPM out and then put it back in. Like restarting windows." He shrugged.

"That sounds ridiculously easy," Simon shouted as the sky flashed.

"It sounds simple but I'm sure there's more to it. If Rodney is successful we'll find out." Elizabeth said pushing herself closer to John in a bid to get some more warmth.

-------------------------------------------------
Steven Caldwell climbed the steps to the gate room just as the balcony doors slid open and three bedraggled figures stepped into the warmth.

"Sir," John exclaimed as he wiped rain off the tip of his nose.

"I beamed directly into the gate room when Doctor Mckay informed me that you were having some problems, but it would seem he's managed to fix it." Caldwell explained.

"I'm going to go and grab a hot shower and a change of clothes," Elizabeth said as rain water dripped onto the floor.

"I second that," John stated.

Simon merely nodded whilst shaking out his clothes.

"Colonel Sheppard, could I have a brief word first?" Caldwell asked in an official tone.

John shared a look with Elizabeth and then stepped forward, "Sure."

"You can talk in my office," Elizabeth suggested.

"Thank you," said Caldwell, "You can brief me with what's being going on in here when you return dry."

As John followed Caldwell into Elizabeth's office and the door was closed behind him, he was beginning to worry that he knew about his relationship with Elizabeth.

He stood stiffly, hands behind his back, still shivering from the cold. His shoulder was aching intermittently.

"You can relax," Caldwell stated as he sat on the edge of Elizabeth's desk.

John did so, crossing his arms over his wet chest.

Caldwell fished into his jacket pocket and produced a white envelope.

"We received this just before we left for Atlantis."

He passed it to John, stood up, and then patted him on the back, "You have my condolences." He left the office and John opened the envelope.

He read it quickly, his eyes greedily taking in every word, and when he had gleamed the nature of the letter. He read it again.

His father had died.

He felt unexpectedly dizzy, his heart was racing and his hands had become sweaty.

He reached out for the chair in front of him, his fingers brushed it lightly and before he could stop himself he fell to the floor and was engulfed in darkness.

TBC

This story is very twisty and all loose ends will be tied up…………..so…..John's going back to Earth :D