A/N: Spoilers through S4's Lifeline

Aftermath

God, he had a headache.

John shuffled across the bridge from Elizabeth's office to the control room on his way to staff meeting, laptop in one hand and a cup of coffee in the other. If the IOA took much longer to choose a replacement, he was going to resign his commission and take the El'ris up on their offer to become royal chauffeur. He squinted at his watch, frowning as his eyes took their sweet time to focus. Ten minutes. He shivered when he entered the conference room; it was absolutely frigid. Afraid icicles would form on his nose, he leaned out the door and caught Chuck's eye.

"It's freezing in here. Can you fix that?"

"Sorry, sir," Chuck replied. "Environmental controls are on the fritz today."

John closed his eyes in defeat. "Of course they are. Just… see what you can do."

He massaged his forehead with two fingers as he fell into his chair with a sigh. Repairs weren't going fast enough. As soon as one system was fixed, another would go down. After opening his laptop, he scrolled through email – all seven hundred and forty-six messages of doom – until the others arrived. Lorne was first, of course. With a crisp nod and a "Good morning, Sir," he took his normal seat on the right, closest to the door. Teyla was behind him, sending a warm smile John's way before sitting on his left. One by one, they filled the room: Zelenka, Keller, Ronon, and, finally, Rodney.

"Nice of you to join us, McKay."

Rodney plopped into the only seat left with a hmmph, managing to balance a muffin on top of a 'Physicists do it in Four Dimensions' mug on top of his tablet. "We've got a few things going on, in case you haven't heard."

"Oh, I've heard," John said. "And smelled and tasted. Since you're last to the party, why don't you start?"

Crumbs dribbled from the corner of McKay's mouth as he chewed. "Repair crews are working as fast as they can. Most of the unstable areas have been shored up, and about a third of the demolished structures have been rebuilt. We're expecting another construction crew from Midway later today. The Daedalus is on its way with the materials needed to rebuild the portions of the city damaged by asteroids. I've got science teams in every part of the city working to replace leaking power conduits." He took a big gulp of coffee. "And before you say it, yes, I've noticed the system glitches. The wiring in this place is a bit old, and it didn't take kindly to slamming into the ocean."

John rolled his eyes. "You've really got to let that go, McKay. Lorne?"

"Yes, Sir. I estimate that we've covered about half the city so far, but going room by room can be a challenge in some of the outer regions. I had Hollister send the notes and photos to Dr. Zelenka."

"Which I received," Radek said. "Thank you very much, Major. Knowing how much damage each piece of equipment has suffered helps us determine which tools and parts to take with us when we begin repairs."

"The men are ready to get back out there, Sir," Lorne said with a nod in the direction of the gate. "Say the word."

John chuckled tiredly. "I wish. But I need the city in working order first. Keep at it, Major. Dr. Keller?"

"We're seeing increased traffic in the infirmary. It's primarily the construction crews, but several of the scientists have come in with electrical burns, and a few of the Marines are, ah, getting a little cabin fever."

"That's not too surprising. Maybe some advanced combat training will cure it. Ronon?" At Ronon's wolfish smile and nod, John turned back to Keller. "How are your supplies?"

"We're good. The blood drive last week definitely helped, and when the Daedalus arrives, I'll sign them up, too. The SGC is keeping us well stocked in everything else."

John winced slightly as pain stabbed like an ice pick through his right eye. He covered it by rolling a shoulder then turned to Teyla. "How are the Athosians?"

"Very well. Our harvest will be more fruitful than it has been in many years. I expect Halling in the next few days with the first of the melnas."

Rodney perked up. "Are those the purple berries?"

"Yes. I have already asked Darek to make the pastry you love so much."

"That's the best news I've had in… weeks." McKay's face grew serious as his gaze dropped to the table.

"Any word?" Ronon asked, breaking the deafening silence.

"No." John scrubbed a hand over the back of his neck. "The IOA refuses to let me begin a search. If there wasn't so damn much going on here…." He cleared his throat. "Anyway, we'll have a new commander soon enough, I hope. Going after Elizabeth will be my first request."

Teyla turned to face him fully. "Do we know who the new commander will be?"

He blew out an exasperated breath. "Not yet. They are 'reviewing all the candidates' according to Landry. Then he reminded me how slowly the IOA moves."

"If I may," Zelenka ventured, raising a finger, "I have one bit of good news. Long range sensors indicate the war between the Wraith and the Replicators continues. We noted the destruction of another hive yesterday."

"That is good news." John felt a genuine smile tug at his mouth. "Okay, kids. Keep doing what you're doing. Major, I'd like to see duty rosters for the next two weeks and preliminary off-world team assignments."

"Yes, Sir."

"Dr. Keller, please forward me a list of the injuries received and how they came about. Radek, based on her report, I'd like you to put together a short safety course for the crews we have rotating through here."

At their nods, John pushed to his feet. "Let's get back to it, then."

As the room emptied, John gathered his belongings, intending to follow Keller when he noticed McKay hanging back. The Tylenol would have to wait.

"Something else, Rodney?"

McKay wouldn't meet his gaze. "Do you really think we'll find her?"

Rodney had wrapped himself in guilt from the instant Elizabeth had run from the back of the jumper. The man refused to give himself a break, no matter how many times they had this conversation. John rarely wished that he was better at this kind of stuff, but these days he would give anything to say the words that would assuage Teyla's grief, Ronon's anger, McKay's self-recrimination…. Hell, if it weren't for the massive amount of repairs needed, he suspected the entire expedition would be curled in a fetal position.

"She's out there, Rodney. She knows we'll come for her."

"It's been almost two months. Do you think she's still alive?"

John leaned a hip against the table, the ever-tightening vise around his head threatening to pulverize his brain. "Until I have proof otherwise, yes. She wouldn't give up on us, and we aren't giving up on her."

Rodney's eyes slowly lifted, filled with remorse. "If I hadn't…."

The headache spiked, and John clenched his eyes shut with a groan. He couldn't do this right now. "McKay, I-"

"What's wrong with you?"

"A headache. It's nothing." John pushed away from the table. "I was going to get some Tylenol from Keller."

"I'll come with you."

"That's not necessary, Rodney. It's just a headache."

"And the last time you had a headache…. Oh, my God. Are there whales on this planet? Has anyone checked? Maybe there's some other indigenous-"

"McKay!" John swallowed his irritation, recognizing the fear in Rodney's voice. "There's enough going on without panicking about whales."

"It's just that I have a- Never mind." McKay grabbed John's arm and hustled him toward the door. "Let's have Keller check you out."

Deciding to humor Rodney, John allowed himself to be escorted to the transporter. The doors closed, and a bright light whisked them away when John pressed the control panel.

"What the hell area did you select?" Rodney asked as they stepped out into a dark corridor that smelled like old gym socks.

John stared at the empty hallway in surprise then turned to the control panel. "I selected the infirmary wing. This shows we're on the outer edge of the city."

McKay stomped back into the transporter. "Maybe you need reading glasses. Men your age start going downhill rapidly, you know." He stabbed at the controls.

When the doors opened again, Sheppard arched a brow at him. "Maybe you're right. Men our age and all that."

"Oh, what now?" Rodney clicked his ear piece. "Radek! What's wrong with the transporters?"

"We have had no reports. What are you experiencing?"

"Sheppard and I are trying to get to the infirmary. First we were sent to the labs beneath the north pier. Now we're in section L47 level 38, near zoology."

John braced a hand against the wall as the argument between the scientists continued. How many more things could possibly go wrong? In response, his headache spiked again causing his knees to buckle. Rodney halted in mid-sentence as John slid down the wall, cradling his head in his hands.

"Sheppard! Radek, you've got to figure out what's wrong right now!"

"McKay," John whispered, "hold it down."

"Yes, yes. Sorry. What do you want me to do?"

"I don't-"

"Rodney!" Zelenka interrupted. "There is a system fault in the transporter controls."

"I know that, Radek." McKay rolled his eyes as sarcasm dripped from his voice.

"No, no, not a simple error. The programming is being rewritten to send you to random areas of the city."

"Being rewritten? Who's doing it?"

"I don't know. I cannot access that information or the program itself."

"Dammit! Some of the transporters go to unstable areas. Can you shut them off? Lock them down so they can't be used?"

"I think so. Yes, is done."

"Chair room," John mumbled, lifting his head slightly.

"That might work." Rodney snapped his fingers as his eyes lost focus. "We should be able to access Atlantis directly, see who's messing with her systems." He caught John's eye. "One… minor problem. We're over a mile away from the chair room."

John extended a hand. "Help me up then. We've got a long walk ahead of us."

"I was afraid you were going to say that."

Rodney grasped John's wrist gently and pulled. John stumbled, leaning heavily against McKay as vertigo swept over him and his brains threatened to leak out his ears.

"You need to go to the infirmary," Rodney hissed.

"Is it on the way?"

"No, but-"

"We need to fix the city. If there is an emergency, the doctors and soldiers have to be able to reach affected areas quickly."

"Then I'll have someone meet us in the chair room."

John wavered as the room spun. "Fine," he agreed. "Make sure they bring Tylenol."

"I'll make sure they bring the entire pharmacy. Radek, we're headed to the chair room. Have Keller meet us there ASAP."

"Right away. Good luck."

"Thanks." Rodney cut the transmission. "We're going to need it."

"Come on, McKay. Where's your optimism?"

"I had it surgically removed at birth, Colonel Sunshine and Roses. Makes for fewer disappointments."

"That's just sad."

"Mock me all you want, but…."

The doors to the stairwell swished open, and they peered over the railing.

John glanced at McKay. "Level thirty-eight, huh?"

"Yeah."

"Isn't the chair room on level six?

"Four sections over."

"Great," John sighed, rubbing his eyes. "This shouldn't take long."

"No more than an hour. Two tops."

"That's was almost positive, Rodney."

"Can you do this?"

"McKay-"

"I'm serious, John." Rodney moved between Sheppard and the steps. "You don't look so good, and I can't carry you to the chair room. The last thing we need is you taking a header down the stairs and breaking your neck. Can you do this?"

"Yes, I can do this. Just… if I stop occasionally, promise not to wig out on me."

Rodney sniffed as his chin jutted out. "Wig out? I have no idea what you're talking about."

John smirked at him. "Of course not. Let's go then, Nerves of Steel."

"Oh, har." McKay peeked down the stairwell again and sharply inhaled, holding his breath then blowing it out explosively. "Okay, I'm ready."

Down twelve flights of stairs, cut over to section K, down another fourteen flights, bridge to section J, down to sublevel one, over to section I and up to level six. Both men were drenched in sweat by the time they arrived in the chair room, and John's headache had progressed from a mere knife in the eye to an entire percussive set in his ears. Zelenka was waiting for them, panting and red faced.

"How did you get here?" Rodney inquired.

"The same way you did. Control room is closer, you know. And I thought you might need help." Zelenka handed John a blister pack of pills and a bottle of water. "Plus Dr. Keller and most of her staff are on the way to one of the construction sites – a crane collapsed. Another doctor is coming here with a med kit."

"Why wasn't I informed of the accident?" John asked between swallowing pills.

Radek sighed. "Communications are intermittent. We've been trying to contact you for over an hour."

McKay walked the room, powering up monitors and plugging in his tablet. "Which doctor is coming?"

Zelenka's face pinked as he ducked his head. "Biro."

"Oh, great," Rodney muttered.

"She's an excellent doctor," John said. "She wouldn't be here if she wasn't."

"She's… weird."

John snorted. "Takes one to know one."

"What are you, twelve?"

Sheppard drained the water bottle and chucked it at McKay.

"Oh, very mature, Colonel."

"Are we set?"

Rodney scanned the room. "I am. Radek?"

Zelenka glanced up from his workstation. "I have called up the transporter controls. I still cannot access the program."

John sucked in a deep breath, mentally bracing for the connection. Most Ancient tech required little to no conscious effort on his part thanks to the natural ability that came with his gene. Flying a jumper caused his spine to tingle. But the chair was unique. The dais lit when he stepped on it, and the usual warmth in his skull was a red hot poker this time. He stumbled, reaching for the chair which drew him like a magnet. The chair activated as soon as he touched it and immediately reclined. Tears pricked his eyes as he connected fully.

Chaos. His senses reeled from the assault. Colors, vibrant and swirling, strobed behind his eyes. Alarms whined, rang, beeped, wailed. Prickles raced over his skin. Aromas and flavors assailed him – apple pie, ozone, gunfire.

"-pard! Answer me!" Rodney's voice was distorted, and John wondered how long he'd been shouting.

"'m fine, McKay."

"You don't look fine. Where the hell is Biro?"

John didn't hear Radek's reply as he sunk deeper into Atlantis' systems. His city was screaming in agony, the shrieking causing him to fumble at his ears with a moan. A schematic blossomed in his mind's eye – blinking green for the areas under construction, amber for the leaking power conduits, a steady orange for the sections still needing repairs. But the sickly purple was the most disturbing. It was everywhere – comms, transporter controls, life support, biosensors. Pain shot through his extremities where the repair crews worked, and his heart stuttered as the purple areas grew. The scent of burnt wiring made his eyes water, and a bitter taste filled his mouth.

Hands intruded on John's connection, clawing at his arms then his face. He opened his eyes to find McKay yelling his name.

"Wha'?"

"You have to get out of the chair now," Rodney demanded.

"Can't," John gasped, pain stealing his breath. "Atlantis is in trouble."

"Let me do it. You're not well."

"I need you to monitor systems. Help me fix them."

"John-"

"Something's really wrong, Rodney."

A heavy sigh. "Can you tell what?"

John closed his eyes, ignoring the pain as he sorted through the chaos. He passed the asteroid damage, the unusual building materials, and the new ZPM, focusing on the purple. The bitter taste worsened, and he choked on it; hands held his shoulders when his stomach rebelled. The headache spread down his neck to his spine. His muscles seized, turning to rock, and his back arched. Tears leaked from his eyes, and he couldn't hold in a strangled cry when he pulled back the final layer.

There, in an innocuous system used to pipe music through the city. Pulsating black, like a cancer eating away at Atlantis. Pain exploded behind his eyes, and the odor of sulfur settled around him. Bile rose again. More hands clutched at him, steadying him. Voices ebbed and flowed.

"…heart rate has doubled. You need to get him out of there." Tones feminine, authoritative.

"I can't." McKay, panicked and plaintive. "He's in too deep now."

"R'dney?"

"Sheppard, thank God. You have got to let go."

The city wailed in protest, and his entire body shuddered. "V-v-virus."

"I don't care," McKay stated. "Get out of the chair."

"No. The city has to be fixed."

"Sheppard, dammit!"

"Can you show us where, Colonel?" Radek asked.

John frowned, fighting against the black tendrils that were snaking into every system and reaching for him. Finally, a visual representation appeared over his head. "Replicator."

McKay spluttered in protest. "How is that possible?"

An image of the Replicator beam striking the tower flashed in his mind. "Signal on beam activated virus."

"You mean it's been here all this time?"

"Yes. Dormant."

"God," Rodney breathed. "I really hate them."

"Colonel Sheppard?" Biro leaned in toward his face, the odd woman completely professional. "I'm monitoring your vitals, and I'm concerned. Your heartbeat is erratic, your blood pressure is low, and your brainwaves… I've never seen anything like it. Can you detach from the chair?"

"No," John whispered. "The city needs me."

"How so?" Biro asked. "Tell me what's happening."

John closed his eyes, watching a battle only he could see. "Atlantis is fighting the virus. She needs me to distract."

Atlantis, a fiery silver-red, blazed as it smothered the purple, wiping out the virus' changes and restoring systems. A soothing blue appeared when Rodney and Radek joined the fight. John turned his focus to the black, unknowingly gripping the arm controls. Envisioning himself in a jumper, he dove at the heart of the cancer, firing mental drones at it. The black roared in protest and rushed at him, bringing an odor of decomp and an acidic taste with it. John spun away but not before a tendril lashed at him, slicing across his shoulder blades. He screamed as agony raced along his nerve endings.

Hands and voices broke through again.

"…not sure how much more his heart can take…"

"It's working, Rodney! The systems are repairing themselves."

"God, John, please stop."

The terror in Rodney's voice registered. John cracked his lids open, surprised to find Ronon holding McKay back. When had Ronon arrived?

"He knows what he's doing, McKay," Ronon murmured.

"He's dying."

"John, can you hear me?" Teyla moved into his line of sight, holding his face in her hands. "You must stop. We cannot lose you, too."

"Can," John mumbled. "Can't lose city."

"We're not losing either one," Ronon stated, releasing Rodney and moving to grip John's shoulder. "Fight."

His attention divided, John didn't see the black tendrils sneaking toward him. He gasped as they leapt simultaneously, the pain too great for him to scream. He was being flayed alive from the inside. His body convulsed under the strain, and his team's voices faded. Curling into himself, he sought the silver-red flash of Atlantis, relieved to see the last of the purple vanish beneath a wave of blue. He pulled in one ragged breath after another, refusing to give in. Mentally climbing to his feet, he pieced the jumper around himself again, grasping the controls with the little strength he had left. He focused, fired every virtual drone he had. The black thrashed under the onslaught, lashing out in one last effort. John braced himself, knowing he wouldn't survive the attack.

"Sorry," he whispered. "Tried."

Silver-red enveloped him. The blow was staggering, but Atlantis absorbed most of it. Silver-red swirled around him, its energy whipping his hair and clothing, then flung itself at the black. Howling, the black struggled as Atlantis wrapped herself around it and squeezed. Black tendrils plucked weakly at the silver-red then fell limp in a cloud of sulfur. John watched the black wink out of existence, taking the foul odor and taste with it. Atlantis swathed him in gentle silver-red, her shrieks fading to a faint melody of victory as she returned her attention to the blinking green construction.

John's breathing hitched as Atlantis released him. The chair righted, deactivating, and he slid into the arms of his team.

oOo

Awareness returned slowly. A steady beep was almost drowned out by rumbling snores. Swirling colors retreated and reformed into the muted hues of the infirmary as John slowly blinked, seeking the source – Ronon sprawled in a chair, legs outstretched. Teyla lay on the bed to John's left, curled on her right side with one hand reaching toward him. He inhaled deeply, wrinkling his nose at the scents of antiseptic and… coffee? Rolling his head to the right, he spotted McKay perched on a stool, cup in hand, eyes distant and expression vulnerable.

"Hey," John whispered hoarsely, smacking his cracked lips and coughing.

Rodney's eyes widened as they focused on him. "Are you okay?"

John nodded. "Thirsty."

"Oh!" McKay hopped up, exchanging his cup for the water glass on the bedside table. He held it for John who sipped gratefully through a neon yellow straw.

"Better?"

"Much." John sat up suddenly. "The city?"

"Fine. You did it. The virus is gone, and the systems are back to normal. How… how do you feel?"

"Much better. Headache's gone. My back itches though, and my stomach feels a little strange."

"Keller isn't sure what happened. When you fell out of the chair, you had huge slice across your shoulder blades. And either you swallowed glass or you suddenly developed an ulcer because something cut the hell out of the inside of your stomach."

"Is that why my chest is sore?"

A blush crept up Rodney's neck, and his gaze skittered away, giving John an opportunity to study him. Dark circles under his eyes. New lines on his face. Barely concealed fear flickering across his features.

"What are you not telling me?" John asked.

"Nothing."

"Have I ever told you how much you suck at lying?"

"Really. Everything's fine," McKay insisted.

A chair screeched as Ronon stood. "Your heart stopped. McKay and Biro worked on you for a while."

John stared at Rodney who pushed off his stool and turned away.

"It is true, John," Teyla said. "We almost lost you. Again." Her voice, always so steady and calm, quaked.

"I don't understand."

McKay's shoulders hunched. "It was the chair. Biro thinks it was causing your headache, too. It needed you to help it focus, to bring order to all the systems screaming for attention."

"I still don't-"

Rodney wheeled. "It was sucking the life out of you! Between Atlantis' damaged systems and the Replicator virus, you almost died. You did die."

"We had to save the city."

"I know that," McKay replied, his face bone white. "I do. I just don't think I can do this again. Not now. Not yet."

"I'm fine." John glanced to Teyla and Ronon, surprised to see Rodney's distress reflected on their faces. "Guys, really. You've got nothing to worry about."

"Nothing to worry about?" McKay exclaimed. "How can you say that? Do you- I can't-" Rodney stumbled to a halt and turned away, stopping when Teyla touched his arm and whispered in his ear.

Ronon crossed his arms, staring down at John from the end of the bed. "I had a man in my unit on Sateda. He thought he had to do everything himself. Never could make him understand he wasn't alone."

"I'm not-"

"Yes, you are."

"He is correct, John," Teyla said, sitting on the edge of the bed. She reached for him but pulled back without touching, clasping her hands in her lap. "I understand your feelings of responsibility for these people. I, too, have carried such a mantle. But I had help, a council to support me. You take such chances with your life…."

Rodney pulled his stool close and took a seat. "What she's trying to say is you don't have to do it by yourself. That's how we lost Carson and Elizabeth. Carson locked us out, and Elizabeth ran off by herself. Maybe things would have turned out differently if they'd let us help. Atlantis needs you. Alive and well, not dead in the chair room."

"I'm not dead." John carded his fingers through his hair, searching for the ever-elusive words to express himself. He could see it in their faces – the hurt, the fear, the loss. While he knew he'd made the right call, there were other times in the not-so-distant past when he could have shared the burden and didn't. "Look at me," he demanded, waiting until all three pairs of eyes focused on him. "I know it was close, closer than I'm comfortable with. I didn't mean to worry you, and I'm… I'm, uh, well, I appreciate your concern. I know I can depend on you guys to be there, and while I can't promise that this won't happen again, I'll do my best to… to ask for help more often."

Teyla smiled, a little relief peeking through. "I am pleased to hear it."

"Yeah, me too," Ronon said. "And I added your name to the list of advance combat training. Since it seems like you need a little excitement in your life."

"That's really not necessary, big guy."

Ronon smiled. "I insist."

A smirk slowly curved Rodney's lips. Happy to see a little life in his friend, John arched a brow in his direction. "You added McKay to that list, too, didn't you?"

"Of course," Ronon answered. "McKay's always on the list. He just never shows up."

"Really. Well, let me see what I can do about that, seeing as how I'm in charge and all. At least for the time being."

Rodney looked horrified. "You wouldn't dare."

John grinned at him. "First thing tomorrow, McKay."

"That is so unfair," Rodney huffed. "Give the man a little power, and he becomes a despot."

John leaned back against his pillow and laced his fingers behind his head. "Just call me Palpatine."

"Oh, come on. I have a thousand things to do. You don't seriously expect me… to..." McKay trailed off as Ronon encroached on his personal space. "Fine."

Teyla laughed as Ronon slapped Rodney on the back. "We will leave you to get some rest," she told John. "Once you have finished your training with Ronon, there are a few moves we need to practice."

"I think Keller's planning on keeping me here for several days."

"Ha! You wish," Rodney said, a bit of tension seeping from his frame as he shrugged from Ronon's grasp. "She's springing you tomorrow."

"Let's go, little man." Ronon looked back from the doorway. "See you tomorrow, Sheppard."

Rodney waved as Ronon dragged him out.

Teyla pressed her forehead to John's. "I am pleased that you are well. We were very concerned."

"Sorry about that."

She pulled back to look him in the eye. "There is no need to apologize. You were doing what needed to be done to save us and the city, and it is deeply appreciated. But know how important you are to us, and not as military leader or expedition leader. You." Teyla squeezed his arm lightly. "Good night, John."

"'Night."

John settled in the bed, squirming until he was comfortable. His team, his council, never ceased to amaze him. He thought of them as family, closer than his own blood, and he had hoped they might feel the same about him, maybe a little. But hearing it verbally expressed, seeing it in the faces of his friends….

Smiling, he turned on his side as sleep tugged at him. He had been trying to shoulder the load alone. He should have known he could count on his team to help him. Confident they could handle whatever Pegasus threw at them, John drifted off, a faint melody of victory singing him to sleep.


Written for the shepsatlantis second annual ficathon for karrikln1671. Prompts: John, gene, angst. Many thanks to kristen999 and kriadydragon for the beta. All faults mine.