A/N: I'm back. I think that I should really begin with apologies for the sheer amount of time that it's taken me to update this. This chapter has been a complete pain, and no matter how many times I tried to write it, I had gotten to a certain point and was completely stuck. Thankfully, finally, it's written, and I can go forward into the next chapter which I'm quite excited about. Anyway, if you're still reading this after so long, thanks for sticking with me.

Chapter 7

"Major"

If Lorne was surprised to see him and Rodney he covered it well. "Sir. If you don't mind me saying so, you look like shit."

This was why he liked Lorne. He wasn't afraid to voice his opinions. He and Nick had become close since his appointment as John's second in command, John wasn't hot on the whole idea of not fraternising with his subordinates, and with such a closed society as Atlantis, it would be implausible.

"Thanks. If I look half as bad as Rodney, then it must be bad."

Lorne couldn't help but smirk as Rodney continued to stare off into space, John's insult clearly not having sunk in, until, "Hey. That is so unfair. Besides it's all your fault."

"My fault, how do you figure that out?"

"If you'd just handed your coffee over none of this would have happened."

Lorne had no idea what they were talking about, but he figured that it must have something to do with the two marines that had joined them, but he thought it best not to ask. Nick decided that it would be a good idea to change the subject, because he knew from experience that if they were allowed to continue they would be here for a long time.

"Ready to break in the newbies."

Sheppard raised a questioning eyebrow at Lorne's use of the word newbies.

"Not really. I could think of a few things I'd rather be doing. Sleeping being one of them." As if on cue he couldn't stifle the yawn that escaped his lips.

"I could certainly think of a dozen projects that I should be spending my valuable time on. But apparently I can't be trusted. I mean honestly even after two days without sleep I'm no more dangerous than the rest of those morons. Besides it was totally different when the Wraith were on their way, then it was McKay you've hardly slept all week but we need you to fix this nuclear bomb."

John couldn't argue with that, but Rodney had only been allowed anywhere near that bomb out of sheer necessity. This time was different, this time someone had already been injured because Rodney hadn't been concentrating. Granted it had only been Kavanaugh, but next time it could actually be someone John liked.

"McKay, how many of those morons as you so fondly refer to them have blown up the labs and Kavanaugh along with it."

John was slightly disturbed that Rodney actually had to think about his answer.

"Seven."

"What?"

"Seven is the number of times Kavanaugh's been blown up in the lab. But if we're talking explosions in general, then I would have to say that it would be closer to thirty."

"And I thought my job was dangerous."

"Rodney, I am surprised to see you down here." Rodney turned to find Radek Zelenka walking down the corridor towards them.

"Radek. What the hell are you doing down here?"

As much as Rodney was surprised to see Radek, Lorne seemed to have been expecting his arrival. "You here to do the orientation for the new scientists, doc?"

"Yes, as always."

"Wait. What new scientists? Nobody told me, and surely as head of department, greeting them would be my job."

"You would think so, yes. But after you left the last batch we received down here for hours, I figured it would be best if I did it."

"Yes, well, that was only because I was extremely busy, and lost track of time."

"Please, you fell asleep at your desk. Again."

"Hmm." Rodney began to stare off into space, and John was wondering if he was thinking about curling up in a nice warm bed, and going to sleep without being electrocuted. It had only been 54 hours since he'd last slept, but it was already too long. Sure they'd gone without sleep before, but only because of the threat of the Wraith bearing down on them, and of course it didn't hurt that Carson had been dosing them up with stimulants. They'd asked, of course they had, for something to keep them awake but he had refused, saying something about not knowing how stimulants would interact with the devices.

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

John took in the excited and nervous faces of the new personnel as they disembarked from the Daedalus. None of them seemed to have noticed the presence of the party awaiting them, all too in awe of their surroundings to pay attention to anything else.

He couldn't explain it, had no idea where it had come from, as he felt a sudden, irrational anger at the people in front of him, still completely unaware that they were being watched.

What the hell did they think they were doing? They had just arrived on a completely alien planet, and were currently standing in an alien city, where, no doubt they had been briefed, anything could happen at anytime, and they were acting as though they were on a sightseeing tour.

Glancing sideways at Rodney he saw a trace of something, not his own anger reflected back at him, but frustration, probably due to the fact that he was being ignored, Rodney certainly wasn't the kind of person who was used to being ignored. In fact John was sure Rodney's silence couldn't last much longer.

One….two…three…

"Oh for," Rodney's voice cut across his thoughts, and John couldn't help smiling slightly as Rodney scowled at him. "What? Seriously Colonel, can't you yell at them or something. Just because I'm not currently allowed in my lab, doesn't mean that I don't have anything better to be doing than waiting for these idiots to realise that their bosses are watching them.

Ignoring him, John turned back to face the hangar deck, to find that there was no need for him to do any shouting, yet. Rodney's tirade, as he knew it would, had had the desired effect. Rodney wasn't exactly best known for his discretion, and the new recruits, obviously having heard him were now looking in their direction, the silent fear, mixed with awe visible on their faces.

John took a moment to really look at the men, and women in front of him. They all looked so young, too young; there were probably some fresh out of basic training. Out of the corner of his eye he could see Rodney scrutinising his own scientists, who were huddled together, as far away from the military personnel as possible. Rodney's forehead crinkled slightly, and John wondered if Rodney was thinking the same as he was, but then again, knowing Rodney, he was probably off in his own little world, solving some physics problem or another, and what he had taken for a scrutinising look, was just the look he got when he was concentrating.

A glance to his other side showed him that his second-in-command had noticed the problem. Atlantis was essentially a colony. They were, for the most part, alone. The new scientists had already begun to isolate themselves, and that just couldn't happen. John had always considered the role of the scientists on Atlantis to be equally as, if not more important than that of the military. As far as he was concerned the most important role of any of the military personnel was to protect the civilians, and he needed to make sure that this new batch of recruits knew that.

Taking a step forward, John felt the irrational anger rising up in him again, as the marine assigned to 'guard' him stepped forward too. Ignoring the urge to scream at the marine, John took a deep breath before continuing.

"Okay, listen up. My name is Lieutenant Colonel John Sheppard, your commanding officer." He indicated first to "Major Lorne, my second. This is Dr. Rodney McKay, and Dr Radek Zelenka. Atlantis is like no other posting you have ever been on, you will see and do things during your stay here that you never imagined possible. You may think you know it all, that you're prepared for anything, but believe me when I say; nothing can prepare you for this." He couldn't stifle a yawn, and wasn't this getting more than a little annoying. "Oh, excuse me. That being the perfect example. "He couldn't help but laugh at their puzzled expressions. "Never mind, I'm sure you'll understand in a couple of hours, News travels fast around here. Anyway, back to the point. Whilst I expect you to conduct yourselves as the trained military personnel that you are, I'm not really a stickler for the rules and regs. However, there is one rule that I will not compromise on. These two people," he indicated to Rodney and Radek," along with every other civilian on this base are the most important people here. If they tell you to do something, you do it without question, because at the end of the day they're the ones that'll be saving our arses with a crazy, impossible idea at the eleventh hour. These guys achieve the impossible everyday, and it's thanks to them, and the other civilians that we're all still here. I want you to be under no illusions that if it comes to a choice, there is no choice. You'll do everything within your power to keep them alive. No matter what the cost. Are we clear?!"

There was a pitiful echo of "yes sir's" from the group before him, so he yelled again, louder, "I said is that clear?!"

"Yes sir!!" This time it was barked back at him.

"Okay. Relax. Major Lorne and I are going be giving you your room assignments, in the mean time feel free to talk amongst yourselves."

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

John didn't know what he was thinking, or perhaps he wasn't thinking at all, as his left hand reached down to his thigh holster. Before he had time to actually consider what he was doing his fingers had wrapped around his 9mil and he was raising it to take aim at Rodney.

Rodney didn't even flinch, a mark of just how much had happened to him since their arrival on Atlantis.

The silence that had descended eerily across the huge hangar, as all conversation died instantly, and thirty sets of eyes turned his way, was broken only by the distinctive click of a gun being cocked behind him. John smiled inwardly, as he realised that Lorne was aiming his own gun at his head, much the same way he had his trained on Rodney.

"It's alright Major," Rodney called confidently. "He's not going to shoot me; this is just his childish way of getting back at me for this morning. Make me look stupid in front of my new staff, and his macho marines. Well, I'm sorry to disappoint you Colonel, but it's not going to work. Even you aren't that much of a psychopath that you would shoot me over a spilt cup of coffee."

John's anger at his new recruits lack of response to the situation was only increased as he saw them visibly relax at Rodney's words. Just because Rodney didn't believe that John would shoot him, didn't mean that he wouldn't, his second-in-command, Major Lorne, clearly wasn't so sure, and that at least should have kept them on alert.

As he pressed the gun harder into the side of Rodney's head, he saw him visibly pale.

"John, drop the gun!" Major Lorne had responded in kind, with the barrel of his gun now pressed firmly, uncomfortably into the back of John's head.

"Relax Major; I'm not going to shoot him." John replied as though this was all an everyday occurrence.

"Even so sir. You're tired. Clearly not thinking straight. I'd hate for you to do something you'd regret later."

John sighed heavily, before lowering his gun, and placing it back safely into his holster. It didn't matter now anyway, he'd administered his test, and all of the new recruits had failed. He had only five minutes ago finished telling them that they were to do anything, and everything in their power to protect Rodney, and what had they done nothing. If John had been possessed by some alien entity, or something equally as disturbing, (It had been known to happen), then Rodney could have been dead right now, and that thought did nothing to stem his anger.

Reaching forward to pat Rodney on the shoulder, he was stopped halfway as Rodney flinched. "Rodney? You didn't think I was going to shoot you did you?"

"No!" Rodney replied a little too forcefully, as though trying to convince himself of what he was saying. But Rodney was a terrible liar, it was all in the eyes, Rodney had extremely expressive eyes, and no matter how hard he tried, there was just no way that he could hide his feelings.

"I can't believe that you thought I would actually have shot you."

"I said I didn't…." at the sceptical look John was giving him, Rodney stopped mid-sentence. "Okay, fine. Maybe for a few seconds I thought, that maybe you might actually have pulled the trigger. I know I can be a pain in the arse, and you're always threatening to shoot me, but I just ignore it for what it is, a joke. But it's a little difficult to ignore when someone's pointing a loaded gun at your head, especially after this morning." Turning to his other side he said, "Radek, as you seem to think you can do a better job than me, carry on. I'll be in my quarters if anyone needs me, but then again I'm sure that you'll all manage perfectly well without me." With that he turned and practically ran from the room, his guard hot on his heels.

The fact that Rodney, even for a nanosecond could believe that John might actually want to kill him, no matter what the circumstances, made him feel sick to his stomach. As he turned back to face Lorne, he couldn't fail to notice the pistol no longer aimed at him, but still held securely in his right hand, as though he perceived John as a threat. But then again, this was what he had wanted, and now that he stopped to actually think about it, maybe it hadn't been one of his better plans. This would at best mean a trip to the infirmary, and a lecture from both Carson and Elizabeth; at worst a trip to Heightmeyer's office. He doubted if the I'm tired argument would have much of an impact, and not for the first time the idea that the device was doing something more than just not letting him sleep sprang to mind.

"Lorne. Get these pathetic excuses out of my sight. Don't bother assigning them quarters; they won't be staying."

"Colonel, with all due respect; you're clearly not in the right frame of mind to be making any decisions right now. I must ask that you relinquish you gun, and Corporal Henderson will escort you to the infirmary.

"What the…Are you questioning my orders?" John couldn't believe that Lorne was doing this; especially in front of his subordinates.

"Sorry Sir, but yes." The fact that Lorne sounded sincere enough did nothing to appease John. He also couldn't help notice the formal tone with which Lorne was now addressing him. "You just got finished saying how important the civilians are, and then you threaten to shoot Dr. McKay; what else would you like me to do. If it were anyone else you'd do the same. Now please, hand over your gun, and go and let Doc Beckett check you over."

Under different circumstances John would have been proud of his 2IC, but right now he was just pissed. Wordlessly, he reached down towards his holster, and saw Lorne's finger twitch towards the trigger of his own gun. Yanking his gun from its holster, he practically threw it at Lorne before storming from the room.

"Henderson!" Lorne called after the retreating marine following John. "Make sure he gets to see the doc and no detours on the way."

Henderson nodded, before running to catch up with John.

Lorne silently prayed to every deity he could think of that they find a way to get those devices off, and soon. He wasn't sure how much more of this Atlantis could take.

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

Elizabeth rounded the corner to find Rodney sitting in one of the chairs that had been placed outside her office. If he wasn't careful he appeared to be in extreme danger of falling asleep.

"Son of a…." She winced in sympathy at the shock he must have just received, but was stalled from saying anything by the way that he was glaring at her; and that defiantly didn't bode well for the conversation to come. "Oh Elizabeth, finally. Where have you been? There's a madman loose in the city, and you're what? Off taking a leisurely stole."

She would have retorted that in fact she was the one in charge around here, and she didn't have to justify her actions to anyone; had it not been for the fact that Rodney had just said that there was a madman loose in the city. Why hadn't she been informed?

"Chuck?" The technician turned to face her, and although he had been doing his best impression of someone who wasn't eavesdropping, she knew he had heard every word.

Chuck shrugged his shoulders, a quizzical look on his face before replying, "No reports of any unusual activity Dr. Weir."

"What! You mean Lorne hasn't told you?" Rodney asked, incredulous.

"Rodney. What's Major Lorne got to do with this?" Elizabeth was getting more than a little confused.

"He was there. So was, erm…" he pointed to the guard standing behind him, "him. Whatever his name is, oh and a whole bunch of new people. It's no wonder I can never remember their names, the amount of people we get passing through here. Anyway, back to the point, which was Sheppard just tried to kill me."

"Rodney." She began speaking slowly and deliberately as though what she was about to say might be difficult for Rodney to understand. "Punching you in the mess hall can not be classed as trying to kill you."

"Oh for…"he was getting more than a little tired of everyone making him out to be some kind of hypochondriac drama queen. "This has nothing to do with that; although that was bad enough. He just threatened to shoot me in front of all the new recruits."

Elizabeth looked to the guard, Matthews, who nodded slowly, before mouthing "Don't ask." please.

"Why would…" She couldn't finish the sentence before Rodney cut across her.

"I have no idea. One minute we're standing there, the next he's got a gun pointed at me. Besides, what does it matter why he did it, isn't it bad enough that he actually did it."

She couldn't quite believe that she was hearing this; she needed Carson to figure out a way to get rid of those devices, and quickly. This was not the John Sheppard she knew. "Rodney, cut him some slack. He's tired, you both are. You're judgements are impaired right now."

"Exactly. You've got it right there. We're both tired and I'll admit I'm a little cranky, but you don't see me putting a gun to your head."

She had to concede that on that he had a fair point. "Okay, look. I'll speak to John; see if we can't work something out. Where is he now?"

"How should I know?"

"Rodney."

"I don't know or care where he is as long as it's nowhere near me. Okay."

Sensing that she was going to get nothing else out of Rodney, she tapped her radio. "Colonel Sheppard, you and I need to have a talk."

A/N: Reviews, criticisms, whatever, are greatly appreciated. Please let me know if you're still reading/enjoying this. I hope that you are. Thanks again, and see you soon with chapter 8, where I promise the guys will be getting a more equal share of the limelight.