Author's Note: This takes place just before Critical Mass in Season 2, so from now on, it could contain spoilers for any episodes up to that point!

Thanks SO MUCH to the people who already reviewed this. I wasn't sure if I dared post since its my first Atlantis fic!

Chapter 4: Raising Atlantis

Both Dr. Weir and Dr. Beckett agreed to a meeting right away the next morning, but I arrived to find the Control Room in a state of chaos. Commands were being shouted, and scientists were scurrying everywhere, obviously not happy. One, a short, dumpy looking man with glasses, ran right into me, then apologized in some language I couldn't identify. At least, I hope it was an apology and not the man telling me what an utter idiot I was. Above it all came the lovely tones of Doctor Rodney McKay, bellowing at someone other than me for once. Not willing to deal with him so early, I quickly skirted the room and made good my escape into Weir's glass walled office. Both of them were already waiting for me, fortunately, because I stayed patiently in the chair for about one minute before anxiously starting to pace around. In spite of my optimism after leaving Teyla, I hadn't slept at all that night, again. I had lost count of how many nights that made.

"What did you want to see us about, John?" Weir prompted me quietly.

Unfortunately, that was all it took. Days of pure misery and anger came boiling up, unstoppable.

"I've had it with this damn guessing game! I'm not part of anything, no one will talk to me except that insane Canadian, and it isn't helping anything! At least at McMurdo everyone avoided me because of hate, but I could still fly! I knew who I was and what the hell I was doing! Here, I- They- I don't know!"

My outburst fizzled out, spent, and I slumped into the seat, certain I'd just destroyed any chance I had at them agreeing to my way of doing things. My temper had once again made a hash out of what should have been a civilized, adult conversation.

Way to go, John! Now they'll find you the nearest rubber room!

"Look, I'm sorry about that, its just...I need to know what's going on! With or without my memory, I'm supposed to be in charge of protecting this city, and I can't do that." My headache spiked, the pushing sensation returning with a vengeance, and I dropped my head into my hands, unable to continue. Desperately, I tried to hide the pain, not wanting to find myself in a hospital bed once again. Mumbling, I thought of one last argument to try. "Besides, doc, you said I was supposed to avoid stress and this is just adding to it. She won't leave me alone. I can't sleep, can't eat..."

Whoops! Didn't mean to add that last part!

I peeked at the other two just in time to see alarm flash across both faces. Now I'd done it.

"Carson?" Weir immediately turned to the doctor and I had to force myself not to snap. It was my own fault. If one of my subordinates started acting like that, I 'd find the nearest doctor, too. With a weary sigh, I carefully sat up, allowing Beckett to go over me, not even objecting to the penlight. That just seemed to heighten their concern.

"How are the headaches, Colonel? And not the blarney you've been feedin' my staff, either."

Caught red-handed on that one! I'd been studiously avoiding the doctor at my check-ins with the medical staff, unwilling to admit to the headaches, and unable to explain the constant pressure that was fueling them.

"They're not good."

Let him make what he wants out of that, I'm too tired to care anymore. I just want something to make sense again!

Weir chose that moment to let me know that she'd heard the one thing that I'd fervently hoped she hadn't. "You said 'she' won't leave you alone. Who's 'she', John? Atlantis?"

Double damn. She understood what I'd meant, too. With a start, I realized she had spoken from right beside me, where she was kneeling. One of her hands was giving mine a reassuring squeeze. When had that happened? I'm not usually so out of touch with my surroundings. Not since Afghanistan.

"I'm not really sure. I just keep feeling...pressure. Like I'm not doing what someone wants, so they keep pestering. Then, once in a while, everything will just go crazy around me. The lights, the doors, the water in my bathroom... I don't know. Then my headache will spike."

There. They wanted to know the truth, so they got it. Their precious city is acting like a spoiled child, denied what it wants. I just wish she hadn't picked me to bear the brunt of it. Brat.

"What the bloody hell!" Very unhappy Carson.

"Rodney! Come to my office for a moment, please!"

Oh, goody! Just what I need to add to this wonderful day!

"What! Oh, hi, Carson. Colonel. You look like something not even my cat would touch. What'd you do this time?" McKay regarded me for a moment with narrowed eyes.

What I wouldn't give for a nine millimeter right now! I actually put this guy on my team? I must have been brain dead.

Doc must have had a good idea of what I was thinking, because he put a restraining hand on my shoulder, keeping me firmly seated. My gaze became fixed on the floor again as another dizzy spell hit.

This just keeps getting better and better...

"Rodney, the malfunctions we've been experiencing-"

"Yes, yes! I can only do twenty things at one time, Elizabeth! So long as its just doors and such, it'll have to wait. I think the fluctuations that started in the ZedPM last night, which could potentially blow us up, should have the priority, don't you!"

"Rodney!" That was a sharp, clear command that cut off even the apparently bottomless mouth of McKay. "Is it possible that the malfunctions are occurring because the city is reacting to John?"

If looks could kill, I'd have been flayed. I'd just broken his favorite toy.

"The city doesn't know how to react to you! This is your fault! Where were you at about ten o'clock last night? Ah, 2200 hours to you?"

I was met with an intense blue gaze, his face screwed up as if he'd just sucked on a lemon. At least my current memory was working just fine.

"In the mess hall, talking to Teyla. Why?"

"Because that's where the minor malfunctions and haywire readings were at the time. It's your damned brain block!"

"Well, excuse the hell outta me! I didn't ask for this stupid city- AHHH!" I found myself sinking to the floor, head trying to decide if it wanted to implode or imitate a tilt-a-whirl first. I never found out which it would be since my body chose that moment to take pity on me and I lost consciousness.

For a long time, I floated, surrounded by a velvety soft, warm darkness. From far away, voices drifted in, occasional snatches of conversation reminding of the world outside this one. And a face...though I couldn't quite force the features to become clear.

"...malfunctions are more widespread..."

"Carson?"

"...needs rest. I should have..."

"...with Sheppard..."

"Rodney!"

That last, exasperated exclamation in that already too familiar Scottish brogue brought me back around. I was once again in the infirmary, but no big hairy surprise there. What was a surprise was the crazy dance that the lights seemed to be doing. Place almost looked like one of those clubs where the illumination is tied in with the music, going on and off to the beat.

My, my. My very own light show. Enough, as they say, is enough!

Vaguely, some part of me heard Carson arguing with McKay nearby, something about expecting miracles and haggis, but I was too focused on the misbehaving city to really pay attention. In my experience, a child throwing a temper tantrum received a time out, or even a gentle swat on the rear, and it was time that Atlantis learned that. Somehow. Feeling like an idiot, but certain on some level that there was actually something there to hear me, I addressed the ceiling.

"That's enough! Leave the lights and everything else alone. Yes, I'm missing a chunk of my life, and for some reason, you don't like it. No, I don't know what the hell it is you seem to want from me. Deal with it and quit making everyone's life miserable! You're hurting, not helping, so knock it off or I will find a way to spank you!"

"Did you just threaten to warm the backside of a city!"

Dr. Weir's amused voice brought my focus back to my current location just as I felt a wave of...astonishment? Chagrin? It was hard to tell, it was so fleeting, but the lights stopped their antics and settled to a suitable level for my still pounding head. McKay, Beckett, Weir, Teyla, and Ronon were all clustered around my bed.

"It worked, didn't it?" I grumbled, sitting up as Beckett brought the head of the bed up to help support me.

McKay's eyes narrowed at that, but instead of launching a nasty comment at me, he began frantically typing at a laptop perched on my bedside table.

"How are you feelin', Colonel?"

"Better. Hungry." I glanced at the doc, a little surprised to find that my appetite had indeed made a return appearance. "Can I get some food, doc?"

"Aye. I already sent someone." Beckett grinned for a moment, then let it slip, a flash of guilt taking its place. "You were worn down physically from the stress of dealin' with the amnesia. I'm sorry, son, I shoulda caught it sooner, changed our approach. I know you well enough ta know how ya love things ya can't control." He shot me a knowing look while Weir smiled and Ronon grunted. "Yer a strong, independent man, Colonel, an' sometimes I forget ya need more help then yer askin' for. Unlike some, who won't leave me alone."

The last sentence was accompanied by a sour glance at the oblivious McKay, though I really wasn't sure why. I was too busy puzzling out the backwards rebuke I'd just been quietly handed to ask about it.

Did he just call me stubborn and stupid? Wonder what I did to deserve that.

"How long have I been asleep?"

Weir took that one, a reassuring hand once more on my arm. "About twenty-six hours. You looked like you needed it."

Great. At this rate, I'll sleep my life away. Not to mention the very reassuring sight of the commanding officer being taken out of the expedition leader's office on a gurney!

"So how long am I stuck here this time? No offense, doc..."

That got genuine smiles out of all of them. "None taken, Colonel. I'm always happy ta see the backside o' you, too. It's about ten in the mornin' now, so if everything still looks good, you'll be free tonight."

Lovely. More hours of counting lights, beeps, or anything else mindless. I haven't worked out an equation for the number of ceiling tiles in the entire city yet.

"Doc..."

"Before you get Carson really annoyed, I brought some reading for you." Weir interrupted me before I could reach true whine tone. "Mission reports to give you a better understanding of what's been going on around here. You made some good points earlier, even if they were a bit loud. I'm sorry that we didn't talk with you sooner about your own treatment."

Hallelujah!

"I...Thank you, Dr. Weir." Wow. Wasn't expecting that one.

"Please, its 'Elizabeth.' I'm your friend, too, even if my bedside manner needs some work."

"What?"

I stared at her for a long moment, utterly confused. Flushing, she beat a hasty retreat after another pat on my arm. Unfortunately, the computer that she had indicated my reading was on was currently being hogged by a still-muttering scientist.

"Excuse me, I believe that's mine."

Without looking up, or even pausing in his typing, McKay grumbled at me, "I need it, this is important. You've screwed up the city and now I'm stuck trying to fix it. Go away."

Go away! Okay, this ass has gone a bit too far.

"You really are an insensitive jerk, ya know that? I can't help it if my amnesia, which no one will even tell me how I got, has upset your sentient city!"

Well, that got a bit more of a reaction, though being stared at as if I were the dumbest person on Earth...er, Atlantis, was not what I was looking for. Reminded me way too much of the MENSA snobs I used to encounter at school. They had made me positive that I never wanted to be one of them, even if I had passed their silly test with flying colors. Not that I ever told them any of that.

"For one thing, Atlantis isn't sentient. The computer controlling the city simply reacts to the thoughts of those with the ATA gene. The stronger the gene, the more the city can connect with even subconscious thoughts. Second of all-" The man had condescending down to an art form.

"McKay!"

"Doctor McKay, I really believe we should let Colonel Sheppard rest."

"That's enough, Rodney! Yer leavin'!"

My head as voices overlapped, drowning out McKay's increasing shrill tones. I didn't care, as long as they removed him and left the laptop. Which was what Ronon proceeded to do- physically. With a smile of appreciation at Teyla as she, too, left, I settled back to await my meal.

Not really sentient, huh? I wouldn't be too sure about that. For all your vaunted intelligence, I think you're being blind as a bat on this one, McKay.