Author's Note: This takes place after my other two fics, and deals heavily with an OC created in those stories. For it to make sense, you should really read those first. Feedback is always welcome, and much appreciated!

Disclaimer: I don't own or profit from Stargate: Atlantis. This is purely for non-profit entertainment purposes only.

Spoilers: Everything through the end of Season 2 is fair game for being mentioned, especially Critical Mass and Michael.

The Education of Rodney McKay

Rodney's POV

With an irritated snort, I scowled at the screen of my laptop, sitting open on the workbench in front of me. There was a line of text snaking its way across it, seemingly all on its own, and there-in lay my problem. How could I possibly get any work done with Miss Nosy into everything, making stupid suggestions? Wasn't it bad enough that I, Rodney McKay, resident genius and miracle worker of the Lost City of Atlantis, had to deal with the fumble fingered brain dead idiots that thought they were scientists? Why did I get saddled with a pint-sized know it all that wouldn't leave me alone?

Two words. John Sheppard.

"Why don't you go bug somebody else for a while, preferably on the other side of Atlantis?" I snapped, then glanced quickly around, afraid that one of my underlings had observed me talking to an apparently empty room.

Not that I was worried about appearing insane, or such nonsense. I was a genius, people expected me to do things that their limited brains couldn't comprehend. Normal was for others, like annoying fly boys who can't stay out of trouble even when on base. No, I was afraid someone would catch me doing the one thing that I had sworn I would never do. Talk to a member of the least useful section of the human race- a child.

Specifically, the Artificial Intelligence created by the Atlantis central computer, who for some reason that defied logic, chose to manifest herself as a six-year-old little girl nicknamed Allie. I swear she did it just to annoy me. Why else would a computer, with all the knowledge of the Ancients available to it, choose such a useless form? Brat.

'But John said I was supposed to help you with the repairs to the power distribution systems. And if you do it the way you have on the map, it'll just short out again.'

My head started to throb. It had taken over a week for Radek's team to isolate and eradicate the computer virus that had been blowing out Atlantis' systems as fast as we repaired them. Now that it was gone, it my turn. I had been working almost twenty-six hours a day for the last three days and I didn't need someone looking over my shoulder! Or through my computer. Or whatever.

"Just go away! Annoying, pain-in-the-ass kid! Can't even get rid of this one with chocolate!"

With a running mutter of insults, I returned to the mapping I was doing, trying to figure out what to bypass without compromising critical systems until I could get to the unused parts of Atlantis and scrounge some replacements. We really needed to figure out how to manufacture the blasted things, but that would be just a little too convenient, too simple. If there was anything I had noticed about dealing with the Ancients, it was that nothing was ever simple.

Take my best friend, for example. Not that I would ever admit that to him. The man wasn't even supposed to be here, let alone continually saving our collective asses at the price of almost losing his own scrawny one. He could have been MENSA, for crying out loud, and instead the wise-cracking Yank has to go and fly helicopters for a living! What a waste! Even worse, he actually believed he was expendable! At least I had the intelligence to know that this place couldn't run without me and went out of my way to keep myself from getting killed. Colonel Martyr did exactly the opposite, damn the man. I hated the twisting of my gut every time we had to sit and wait for Carson to put him back together again. And now he'd saddled me with the twerp.

My computer screen went blank, wiping out all the work I had just done, and my temper snapped.

"HEY! You stupid little interfering brat! It isn't bad enough that you have to go around hurting people and stealing their memories, now you have to cause me headaches when I'm trying to fix your sorry self! Go AWAY! Nobody. Wants. You. Here!"

The lights flashed twice, then silence descended on my lab. Immediately, I felt a little guilty for what I'd said, but only for a moment. Maybe I could get some work done now, before one of my underlings screwed something else up, or some new alien race decided they had to try blowing up the city. Then it would be the Miracle Man and the Annoying Fly boy to the rescue once again. Aided by Conan and Xena, of course. Somebody had to do the hand to hand fighting. I bruised way too easily.

Five minutes later, I had just begun to reconstruct my work when I heard the door behind me slide open.

I knew it was too good to last.

With a long-suffering sigh, I turned... and confronted the most dangerous thing in all of Atlantis.

An angry Lieutenant Colonel John Sheppard.

John's POV

It had actually started out as a pleasant day. For the first time in two weeks, I was feeling reasonably human. I had been out of the infirmary for two days now, and spent most of that time obediently resting in my room. This morning it hadn't taken long for me to get bored, so I decided to crash my team leader's meeting, which was being chaired by Major Marcus Lorne, my second in command, while I was once again on medical leave. As long as I didn't look like I was about to fall on my face with the slightest breeze, the man wouldn't rat me out to the Scottish Dictator in the Infirmary.

So next time don't get yourself punctured by a madman.

Sounded a lot easier than it actually was, since I hadn't asked for the mess in the first place. The man had apparently hunted me for over ten years before finally cornering me here on Atlantis. He had cracked two ribs, given me a concussion, a bone bruise on my leg, and put both a bullet and a knife into my left shoulder. Everything had healed now, except the shoulder, which was really starting to irritate me. I'm not the type to take well to idle down time, especially when I had ten thousand things that needed to be done. Like checking in with my team leads.

I had sat down, to the knowing looks of several, and the amused wink of Lorne, and settled in to listen. That was when the headache hit, and the entire damned room started spinning. Quietly, I closed my eyes and dropped my head, willing it to stop long enough for me to escape the room. It took a minute, but during a lull, I got up, trying to appear as casual as possible. Must not have worked too well because I heard someone follow me into the hall and halt beside me where I stood, letting the corridor wall hold me up.

"Sir? Do you need me to page Doctor Beckett? You just turned as white as a pair of dress gloves." Lorne, sounding genuinely concerned.

"No, I'm good. This'll pass in a minute. Allie's a little upset again."

That got an understanding nod. "She's a good kid."

"Yeah. Go back to the meeting, Marcus. I'll go deal with this and grab your report after."

"Mmmhmm. Sure you don't want me to stay with you, sir? You really don't look good."

I gave him an exasperated eye roll, which he rightly took to be a dismissal. Ever since Allie's occasional lapses of control had caused me to have physical reactions, everybody seemed to think I needed to be wrapped in cotton like spun glass. If I hadn't snuck out of my room this morning, I would no doubt have had an escort of Teyla, Ronon, Elizabeth, Carson, or Rodney, any combination of them or all of the above. Yet another thing that had me ready to swing one-handed from the rafters. Grounding myself, and firmly swallowing against my rebelling stomach, I walked down the hall to my office, flipping on my new laptop as soon as I sat down.

"Okay, kiddo, what's wrong?"

As soon as I said that, a wave of anger, guilt, sorrow washed through me, and my vision tried to gray out. Crap.

"Allie, I need you to calm down. If I land in the infirmary now, Doc'll never let me out. Now, what happened?"

'Dr. Smartypants.'

The first broken sobs sounded in my ears, though there was no one with me physically. It was a peculiarity of my strong ATA gene that I could actually hear the little girl sometimes, not to mention feel her strong emotions. Somehow, I wasn't surprised at the newly revealed source of this latest meltdown. Rodney wasn't high on tact with adults, let alone a child. I knew that there was a lot of tension between the two, but every time I had the leisure to think about addressing the conflict, another crisis just had to erupt. Looked like I couldn't put it off any longer.

"Just what did McKay do this time? I thought I could actually trust you two to play nice since he's still working on repairs. You do have a fairly unique perspective on the systems."

'He...he said...'

The broken quality to her voice, echoing the written words, began to alarm me. Whatever had happened seemed to be more then just a misunderstanding or a shouting match. My headache kicked up another notch, too, telling me that I'd better get to the bottom of this soon or I wouldn't be conscious to do so. Closing my eyes, I relaxed back into my chair, doing some calming breathing exercises I had picked up during a recent involuntary six month vacation.

"What happened? It's okay, whatever it is, we'll solve it, I promise."

'He said nooo...bboody wwanted meee heerreee...!'

Okay, now I'm going to kick him back to Earth without the Daedalus!

Absolutely furious, I went off in search of the soon to be dead Doctor Rodney McKay, anger doing wonders to clear my head.

Rodney's POV

You've never seen scary until you've seen a furious John Sheppard bearing down on you. The man made a tornado look tame. It's even worse when you don't have a clue as to why he's coming after you.

"Aren't you supposed to be resting in your room? You look like shit, which, while it is a state I've become accustomed to seeing you in, is not really all that good."

Did I mention that I tend to babble when I get nervous? The last time I had seen my friend this angry, he was putting a knife blade through the offender's back not long after.

"I can't rest, McKay, because I have an innocent little girl sobbing her heart out in my head! Now, would you care to tell me why I almost passed out in the middle of my team lead meeting because you told Allie nobody wanted her here!"

I really can't help saying the first thing that comes to mind sometimes, though I've tried to stop myself more than once. "That twerp tattled on me!"

That got me a smack on the back of the head, and not a gentle one either. Even just out of the infirmary, that man is strong. I did have the presence of mind not to object further, instead just mutely facing the angry officer as he moved into my lab and sank down on the nearest chair. I could see the beads of sweat breaking out on his forehead. Stubborn idiot. He was going to faint in front of me because of that girl. Which was one of the real reasons I didn't like the brat. I have a thing about people hurting my friends.

"What the hell were you thinking, McKay? You don't say something like that to a kid!"

I stared at him in shock for a long moment, tempted to actually tell him the truth. Not that it would do any good. When it came to friends, and loyalty, the man only saw what he wanted to see, much like myself when it came to science. The difference was my blinders had been ripped away when my own arrogance had almost gotten us both killed, not to mention destroyed three-quarters of a solar system. His had just gotten thicker. Instead, I settled for the response that I knew he expected.

"Your little friend was getting in my way. I've been trying to repair all the damage that maniac did when he became obsessed with you! Which is...disturbing on several levels in and of itself. I don't have time to be debating everything with some stupid kid!"

That got an exasperated eye role. I noted, however, that his face had gone about as white as the sling cradling his left arm. No, now was definitely not the time to get into this, even I could see that. Especially not where certain small ears were able to listen in. Better to let him think this was just me not liking a child.

"McKay..." He drawled my name in that tone he got when he thought I was being extremely stupid. "She's part of the city you're trying to repair! Don't you think a computer might know something about the systems she can control?"

Damn it, he actually has a point!

But then, computers aren't supposed to act like children and throw temper tantrums. Computers are logical, predictable, dependable, and do exactly what they are commanded to do. Allie was the polar opposite of all those things, and driving me absolutely crazy.

"Fine. You tell her to keep her opinions to herself unless I ask for them and don't throw a snit fit if I don't agree!" I switched my focus to the ceiling. "You hear that? No tantrums! If you want to work with an adult, act like an adult!"

Sheppard's face tightened again, eyes flashing angrily at my demands, but I quickly turned back to my work, hoping the colonel would leave. Preferably back to his quarters to lay down before he collapsed. There were several minutes of silence before I heard him slowly get up, not quite able to suppress the low moan of pain. That sent a jolt of fear and worry through me.

As a rule, John Sheppard doesn't show he's in pain if he can possibly help it. I'd seen him shrug off a bullet wound and being thrown multiple times by a Wraith with a cocky 'I'm good'. Carson had once speculated within my hearing that the man could probably break a bone and not even feel it, not know he was injured, because his pain threshold would kick in, masking it. I couldn't comprehend that. How could someone unconsciously shut off pain to that degree? I'd broken bones before, and they hurt! That he was feeling it enough now to moan, even if the stubborn idiot would never admit it, was a pretty bad sign.

His voice came from behind me, sounding utterly exhausted. "Just...try not to kill each other for a while, okay?"

As soon as I heard the door close, I sat back.

"If you're the one causing him that much pain, I'll find a way to knock your sorry little behind!" I hissed, hoping Allie was present for once. "Make yourself useful and tell Dr. Weir that someone needs to check on Colonel Sheppard. And no more arguing with me!"

'You started it, Dr. Smartypants.'

"Did not!"

'Did so!'

"Did not!"

'Did so!'

"Did- What the hell am I doing, sitting here arguing with a computer! Leave him alone! That's an order!"

Nothing further appeared on the screen and I sat back, smug. Computers are programmed to do what you tell them to. End of story.

All the power went out in my lab, leaving my sitting in complete darkness.

I hate kids!

TBC...

A/N: The speculation on John's pain threshold is based on fact- by personal experience. I actually have broken bones twice without even knowing it because it was masked by my high threshold, which is about the same level that John's supposedly is (according to Carson in Conversion).