Chapter 2.

I'm sorry this has taken so long to be posted. It was written ages ago, but wouldn't play nicely and let me upload. Thanks so much for the wonderful reviews. To answer a couple of questions. Meningitis is the inflamation of the lining of the brain, in this case due to bacterial infection. Septacaemia, or put simply, blood poisoning due to bacterial infection here, often occurs with this illness, and is extremely serious, often resulting in death. Thanks, as always, goes to my wonderful beta, Kodiak Bear Country.

John was confused. He knew he was burning up; his body felt scorched, and spent. His head felt like it was going to explode in the near future, and he was certain something inside his skull was trying to push its way out. He distantly thought he'd never had a headache like this before in his life, as jackhammers competed for supremacy. Everything hurt, his arms, legs, chest, even breathing was painful and surprisingly difficult. He was vaguely aware of a voice talking to him, and of something wet and cool lapping at his body. A dog? Why was there a dog in Atlantis? Sheppard tried to move, but his body wouldn't co-operate. Groaning, he managed to grind out a few words.

"How'd a dog…get here?…like…dogs."

McKay looked down at Sheppard and grimaced. The pilot had begun to thrash and moan in his delirium. John was burning hot to the touch, flushed, yet an alarming pallid complexion lay underneath the superficial pink hue to his skin. His body was drenched in sweat, and Rodney knew Sheppard had to be dehydrated. More purple rashes had begun to appear alongside the blotches in the crook of the sick man's arm. Rodney strained to listen to John's ramblings, and raised his eyes heavenward as he heard the fevered man ask why there was a dog there.

"I don't believe this! There's no dog here, Sheppard, you're hallucinating," he said slowly and deliberately.

Sheppard continued to groan and move sluggishly.

"Is…it's licking…me."

McKay continued to sponge down his friend and stopped as he realised Sheppard's mistake. An annoyed expression came over his face.

"You idiot! That's me tenderly mopping your brow, amongst other body parts. Carson, where the hell are you?" he cried out uselessly into thin air.

Ten minutes later and McKay sighed in relief as the large double doors were prised open. Carson immediately ran in and knelt over his patient.

Examining the prone man, Carson tutted and signalled to two of his staff.

"Melissa, let's start an IV. Shelly have you got the IV antibiotics ready?" Both nurses nodded their heads. "I can't afford to wait till we get to the infirmary. I'm going to give them to him now."

As Melissa guided the needle into the crook of Sheppard's elbow, Carson injected a large syringe into Sheppard's other one. The prone man groaned almost inaudibly.

Carson then proceeded to stick a thermometer in John's ear. After the device beeped he withdrew it and fretted more. 40.5 degrees.

"Colonel. Can you hear me Lad?" No response. "Colonel? I need you to wake up for me." A soft moan. "That's it Son, open your eyes for me," Carson coaxed. Taking his penlight, Carson lifted Sheppard's right eyelid and shone the light in his eye, withdrawing it as the colonel flinched and groaned.

"All right lad. Just relax now. We'll get you on the gurney and take you to that nice infirmary bed, where the nurses will fuss over you," he soothed.

Beckett and his nurses carefully lifted Sheppard onto the litter, covering him with a thin sheet, and then swiftly strapped John in with belts fastened across his chest and legs. Beckett deftly placed an oxygen mask over the ailing man's face and signalled his nurses to start their journey with the colonel to the infirmary.

Rodney walked alongside the procession, biting his lower lip nervously.

"Carson?" he tentatively asked.

"I don't know, Rodney," he replied, understanding what the physicist was trying to ask. "The good news is he's got that large dose of antibiotics in him and some fever reducing medication too. We'll do a lumbar puncture as soon as we get him stable and that'll tell us what we need to know."

Once they'd reached the infirmary, the medical team sprang into action, moving Sheppard to a bed, inserting another IV and catheter, as well as attaching John to various monitors.

A tall fair-haired doctor shook his head apprehensively.

"Dr. Beckett? I don't like the look of these readings, his O2 sats are falling, and his BP is dropping. Shall I start him on some gelofusine?"

Beckett nodded briskly.

"Aye, David. Right, let's administer sux and get him intubated," he ordered, smiling grimly at Melissa who administered the muscle relaxant, before passing the intubation kit to Carson.

Once safely intubated and on the vent, Carson ordered more drugs to be administered, and for bloods to be taken, and set about examining his patient.

Rodney stood to the side of Sheppard's bed in shock, being careful to keep out of the medical team's way.

"All right. Let's roll him and prep for the lumbar puncture. The medical team deftly rolled John into a curled up foetal position on his side, and as Carson swabbed his patient's lower back, McKay winced. "Good. Melissa, you hold the colonel's legs, Shelly hold his shoulders. Okay, here I go…"

Beckett quickly inserted the long needle with a tube inside, and proceeded to position the tube in the correct place. Momentarily, a cloudy, blood-streaked fluid dripped into a small test tube. Passing it to one of his staff, Beckett ordered the sample to be taken to the lab immediately.

After cleaning the colonel up and dressing the puncture mark, Carson and his nurses carefully rolled Sheppard back over. Beckett proceeded to check his patient thoroughly, making notes and recording readings from the monitors in Sheppard's medical file.

After silently watching Carson for ten minutes, Rodney couldn't keep quiet any longer.

"Well?" came an impatient enquiry.

"Rodney, I won't know anything for certain until I get the labs back," Carson admonished the anxious physicist.

McKay scowled. "You must have an idea, a gut feeling?"

Carson studied Sheppard's monitors and checked his IV lines.

"Aye. His spinal fluid wasn't clear, so it's a good bet this is bacterial meningitis." Carson looked McKay in the eye. "Before you have a complete freak out, no, that's not good, and yes, he would have benefited from treatment earlier. No, I don't know what his chances are, and I can't and won't give you a percentage figure. He's very sick, and I've got a battle on my hands." Carson exhaled and shook his head. "What I don't understand, is how a healthy man like the colonel could suddenly develop an illness like this."

Rodney bit his lower lip.

"He seemed a little off yesterday, though he didn't say he felt sick or anything." McKay suddenly considered Sheppard's rapid decline and a worried expression crossed his tense features. "Do you think this could have something to do with the Ancient Device he activated? I mean he seemed a little off his game, but not really sick until the device blew out the power. He got sick and passed out within twenty minutes of him being enveloped in the oddly pretty, green light."

Carson frowned. "I hadn't even thought of that. Did the light touch you?" he asked in concern.

"No, no. I was standing too far away. Could the device have somehow made him sick?" McKay started to pace up and down, wringing his hands in anxiety.

Before Beckett could answer, Shelly interrupted the two men.

"Doctor Beckett? I thought you'd want to see these blood test results immediately. I also got a call from Dr. Henderson, the colonel's spinal fluid has tested positive for bacterial infection, though the bacterial strain is one he says he's never come across before. He said to tell you the bacteria have died, and is decomposing."

Carson bit his lower lip as he absorbed his nurse's words, while simultaneously scrutinising the piece of paper with the lab results.

"Good God!" He visibly paled and shook his head in disbelief.

McKay gulped.

"What?"

"This can't be right! I ran a full blood work up on the colonel two days ago, and everything was completely normal," Carson exclaimed in shock.

"What?" Rodney repeated a little more forcefully.

"Colonel Sheppard's immune system has totally shut down. His white blood count is one point four. How the hell could this have happened?" Beckett wrinkled his forehead in thought. "Rodney? Did you pick up any signs of radiation or anything unusual when the device was operated?"

McKay's face darkened. "Er, I didn't check. All the equipment was out, and then Sheppard got sick."

Carson exhaled. "Right. I need to run some more tests. You need to be examined too. Dr. Lambert will give you the once over."

Carson pointed toa nearbybed, and pushed McKay in the right direction.

McKay sat nervously, and waited for Carson's second in command to examine him. Suddenly realising something, McKay tapped his radio.

"Kavanagh? Is the power up yet?"

The pony-tailed scientist's voice filled McKay's earpiece.

"I'm nearly there. Whatever you and Colonel Sheppard did fried a lot of circuitry."

McKay's brow furrowed in thought.

"Kavanagh, when you've got the scanners working, can you scan for any sign of radiation or anything unusual that would cause a lockdown? I have a horrible feeling Colonel Sheppard and I have just irradiated ourselves."

"Will do. I shouldn't be long now. Why am I not surprised you two clowns would do something like this?" Kavanagh muttered as his com went dead.

Rodney scowled in annoyance at the scientist's words, and frowned, as he suddenly felt dizzy. Lying down on the bed, he turned to see Dr. Lambert approaching.

"Er, I don't feel so good," he complained as a wave of nausea hit him.

The tall fair-haired doctor walked briskly over to McKay.

"Can you tell me what's wrong?"

McKay nodded. "Feel dizzy – had to lie down. I've got a headache too. God, I've probably got radiation sickness!"

Dr. Lambert grinned. "Let's take a look at you before we jump to conclusions," he stated.

-oOo-

Elizabeth rushed into the infirmary in a panic.

"Carson?" she called, as she approached the anxious doctor. "How are they?"

Beckett led Elizabeth to a chair and pulling up one for himself, gestured for the woman to sit down.

"Rodney is a little under the weather. Our tests have shown he has a slightly diminished immune system and is suffering from a simple cold-like virus." Carson grinned wickedly. "Naturally, according to him, he's dying and won't be with us much longer. I've given him analgesics and put him on an IV to be on the safe side, but otherwise he's showing no signs of radiation sickness – in fact they're both clean in that respect."

Weir nodded in understanding. "That's good. And John?" she asked nervously, knowing her second in command always had to complicate matters.

Beckett grimaced. "He's not so good, I'm afraid. His immune system has been totally wiped out, a bit like someone may experience when they're on chemotherapy. It seems he had contracted a previously unidentified bacterial infection, which quickly overwhelmed the colonel's body, resulting in the meningitis." He stopped to run his hand through his hair. "Unfortunately, his immune system has to all intents and purposes, been switched off, meaning he's incredibly vulnerable to further infection. Fortunately for the colonel, the bacteria have been destroyed, but I've no idea how that's happened. It seems too much of a coincidence that twenty minutes before his collapse he was enveloped in green light from an Ancient Artefact he activated."

Weir nodded her head again, and bit her bottom lip. "If the bacteria's been destroyed why is John so sick?"

Carson frowned. "The toxins from the decomposing bacteria are poisoning him, and there's not much I can do. If you combine that with his compromised immune system…" Beckett paused and tiredly rubbed the back of his neck. "As you know, Dr. Zelenka has returned to the planet with a team to see if they can find anything out about the artefact, hopefully they'll be able to tell us something useful. I've got the colonel on the strongest antibiotics possible, but seeing how the bacteria has been destroyed, it's probably not necessary. I'd rather not take any chances." Carson stood, and pushed the chair against the wall of the infirmary. "I'm giving him immune bolstering treatments, and am supporting him with medication to try and combat the toxicity he's suffering. I may have to put him on dialysis, as his kidneys are starting to fail. He's been isolated and I'm having him barrier nursed. Unfortunately, I'm very limited in what I can do here. I could really use Rodney's help with researching the device, but he's not feeling very well right now."

Weir stood, and grimaced.

"Do your best. Hopefully Rodney will recover soon. Keep me informed, Carson."

Beckett smiled. "Aye, I will."

-oOo-

Rodney felt terrible. His head pounded, his nose was blocked, and he felt dizzy, weak and wiped out. Spying Carson approaching, he groaned, and frowned when the doctor hovered a considerable distance away from him.

"Carson? I'm dying here. Why haven't you broken out the good drugs? Sheppard always gets them…"

Beckett exhaled. "Rodney, I know you feel like crap, but you've only got a nasty cold. I can't come near you, as I don't want to pass your virus on to Colonel Sheppard. I've brought you a decongestant, which Shelly will give you, and hopefully that will make you feel a little better. I really need your help."

McKay looked at Carson's serious face.

"Sheppard?" he croaked miserably.

"Aye."

McKay listened quietly to Carson's findings and winced as he learned of Sheppard's situation.

"Give me something stronger and get me on my feet. I'll go to the lab and work with Radek when he gets back." He sniffed, as he managed to sit himself up.

Carson shook his head.

"I don't think that's wise, Rodney. I just wondered if you can tell us anything about the device that may help?"

McKay flopped back down.

"Er, there were no warnings on it. Sheppard activated it easily, it hummed, spewed forth a pretty green beam, which enveloped the colonel. The power went out, and then the lockdown occurred. Why would the city go into lockdown?" Rodney mused.

Carson furrowed his brow in thought.

"May be it detected the bacteria in the colonel?"

"Yes, but presumably Sheppard had been infected with the bacteria for at least a day?" McKay's face showed his confusion. "This doesn't make sense - the city would have gone into lockdown as soon as it detected something dangerous." McKay sneezed and blew his nose on a tissue he'd been holding tightly in his hand. "Hang on a minute. I'm missing something here. Sheppard was a little off yesterday, and not himself today, right?" Rodney frowned. "That doesn't mean he had the bacterial infection then. He might have been feeling a bit pre-menstrual or something." McKay sniggered at his own joke.

Beckett huffed in annoyance at the physicist's attempt at humour.

"I'd hardly call the colonel hormonal, Rodney. You on the other hand often exhibit monthly mood swings. Or perhaps it would be more accurate to say daily ones…"

McKay gave Beckett a withering look.

"Oh, yes. Insult the dying man!" Rodney yanked his sheet up under his chin, and continued. "What if the device gave him the infection?"

Carson's face showed confusion.

"What would be the point in that, and what about his immune system?"

Rodney grimaced.

"Well, we did find the device in an Ancient research lab on another world. They could have been tampering with new forms of bacteria, or even creating them?" McKay suddenly sat up straight. "What if this was some sort of biological weapon?"

"I don't believe the Ancient's would create something like that, Rodney. It doesn't seem to fit in with what we know about them," Carson resolutely stated.

McKay snorted.

"Really? I'm not so sure about that. They certainly had a hand in creating the Wraith didn't they? They also seem to not want to dirty their hands with any of us now, do they? They just float around enjoying the Universe, ignoring all of the suffering us mere mortals endure…"

"I get the point," Beckett interrupted Rodney's little rant.

McKay blinked in surprise. "Oh, yes, well – good," he stuttered. "Well, as I was saying, this could be a weapon. Maybe it's linked to the Wraith? Perhaps the device is a failed experiment?" he mused.

Zelenka rushing up to them interrupted both men.

"I've found out what the device is for, and more importantly, I have a cure for the side effects the colonel is suffering!" the small, bespectacled Czech exclaimed.

Zelenka smiled broadly and pushed his glasses up the bridge of his nose with his hand.

McKay huffed impatiently.

"Well? Don't keep us in suspense. Some of us are dying here." Thinking better of what he'd said, Rodney blushed. "Well, one of us actually could be…"

"The device was originally a prototype weapon, and…"

McKay smugly interrupted Zelenka. "I knew it! Ancient's too nice to make weapons my…"

"Rodney! Let's listen to what Radek has to say," Carson admonished a very gloating- faced McKay.

Zelenka grinned at Carson. "Thank you. As I was saying…It was a prototype weapon, but was abandoned, as it had disastrous side effects. The idea was to infect the Wraith with a deadly strain of bacteria. It would only kill the Wraith, and all other life forms would be unaffected by it. However, the strain mutated quickly and became dangerous to all life, even the Ancient's." Zelenka grimaced. "A whole team of Ancient scientists died before a cure was found. Though the bacteria died very quickly once infection had taken hold, it still killed the victim as it released deadly toxins and annihilated the immune system."

McKay snorted.

"Yes, well, I'd managed to work most of that out all by myself. So, why wasn't I infected by the bacteria, or anybody else, for that matter?"

Zelenka looked at McKay.

"I have hypothesised that the artefact the colonel activated malfunctioned, and instead of dispersing the bacteria by creating a widespread beam, it simply misfired sending out a huge energy pulse, but the beam with the contagion just enveloped the colonel alone. That is lucky for us, but unfortunate for him. If this weapon had been deployed as it was designed to – well, we would probably all be dead or dying by now," Zelenka said gravely.

"So why has my immune system been affected? If the bacteria didn't infect me, there's no reason for it to be compromised…" Rodney mused.

Carson chewed his lip in thought.

"It's possible you were a wee bit under the weather and have contracted a cold coincidentally. You could be a red herring here, so to speak. Your immune system was only slightly under par, after all."

McKay nodded, and then grimaced.

"That would make sense. Though I don't think it's fair to say I'm a little bit under par, Carson. I'm really sick…"

Carson exhaled and frowned in concentration, ignoring the complaining physicist. "You said there is a treatment we can administer to Colonel Sheppard?"

Zelenka looked startled. "Yes. I am sorry, I should have explained this to you immediately." He rummaged in his rucksack. "Here are written instructions I have made from translating Ancient texts I found. It tells you what you must do. Only a carrier of Ancient gene can use it." Radek held out a crumpled piece of paper and a long, cylindrical, metal object, which had buttons along one side, and narrowed at one end. "This is device which will hopefully cure the colonel, though it may take days for him to recover, and he will be very sick for a while."

Beckett read the piece of paper and studied the device, which he surmised was a piece of medical equipment.

"Do you know how it works?"

Zelenka smiled apologetically.

"I have no idea. After Colonel Sheppard is cured, I will research it for you, but I thought it best to bring it to you immediately."

Carson nodded.

"You did the right thing. I'll take this to the colonel immediately."

Beckett walked to Sheppard's bed and frowned in concentration as he remembered the instructions. He pressed a series of buttons and pressed the device against Sheppard's neck. John tensed momentarily, as the device emitted a low whirring sound. Carson withdrew the device and the colonel instantly relaxed.

"I think that's it. Now, we wait," he stated solemnly.

Tbc.