Disclaimer: I don't own Atlantis. 'Nuff said.

Chapter 3

John sat on his bed contemplating sleep, it hadn't been coming easily of late, and the nightmares had changed from visions of Elizabeth to images of Emily. After what happened in the infirmary a week ago, he just couldn't risk asking Carson for more sedatives, not that drugs were his first choice. He'd tried everything, running, working late, early mornings, he even considered jumping off the north pier for a quick swim, until Rodney pointed out that the water was so cold he'd die of shock before he managed to swim anywhere.

"Rodney!" John sprang to his feet, the scientist was never asleep, and since he'd been demoted he was always happy for company.

Wandering out of his quarters, he found the nearest set of stairs and set off for the research lab at the bottom of the main tower, walking killed time, and time was something he had a lot of at the moment.

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Laura Meyer was in her office going over the report of Emily's disappearance; she couldn't believe the incompetence of the military. Colonel Sheppard was one of her pet hates, his whole attitude irritated her, and he made it painfully obvious he would never accept her the way he had the wonderful Dr. Elizabeth Weir.

Her musings were cut short by an incoming transmission, glancing at the screen she noticed it was a secure channel requiring an authorisation code. Frowning she locked her door and entered the obligatory sixteen digit code.

"Confirm identity!" The expressionless voice demanded when the channel connected.

"Laura Meyer, fifteen seventy-three, alpha, four, one, six." She responded, keeping her voice neutral, any change of pitch would mean she was not alone, and the connection would not be made.

"Identity. Confirmed. Connecting."

"Meyer, good evening." A thin, blonde haired man appeared on her screen, "Time for your weekly report I think."

"Good evening, a very little to report I am afraid sir," Meyer replied, a edge of disgust in her speech, "Turner is still missing, the military are incompetent and that Sheppard man needs to be sacked!"

"We cannot move him Laura, you know that. He was placed by the military not by us, besides he as the ancient gene, he could yet be useful."

"All our people have had the ATA gene therapy sir, they.."

The blond man cut her off, "He's got the original gene, he's the only one that has successfully managed to operate the control chair, and other systems in the city work for him that don't work for anyone else! More to the point WE cannot dispose of him without attracting attention. Give it time, is he still unstable?"

"Yes, for the moment, but he appears to be improving, so I can't put him down as being unfit for duty."

"Ignore him then, we have more pressing matters to attend to. We're increasing speed, time for the next phase."

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To get to Rodney's new lab, Sheppard had to cross the control room, which at this time of night was practically empty, only the ghost watch was there, guarding over the city whilst it slept.

Out of habit he glanced up at Elizabeth's office, half expecting to see her busy at work or standing on the balcony, cup of coffee in hand. She wasn't there of course, but a light was on. Straining his eyes he could see Meyer sitting in front of her computer, seemingly talking to it, which was a crazy thought for sure, as the wormhole wasn't open, meaning no messages could be sent or received. 'She's going crazy' he thought, but stored the information away, determined to ask McKay about it when he saw him.

He turned away, preferring to keep moving than stay anywhere that was in her company. He mooched across the room, nodding to the team as he went, ignoring the curious looks at his odd behaviour. Pausing before the door he turned, a strange feeling raising the hair on the back of his neck, "Elizabeth?" he whispered as he looked at the gate, then an expression of immense sadness clouded his face, he sighed and shook his head before passing through the sliding door, and on down to Rodney's lab.

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Rodney McKay was analysing some results when there was a knock on the door and Colonel Sheppard walked in.

"Hey Rodney, what ya doin?"

"I'm analysing results, what does it look like I'm doing? Practising my tap dancing skills?" He snapped, irritated at having to do such a boring job, "More to the point, what are you doing, shouldn't you be in bed or something?"

"Yeah I guess so, but I was bored and couldn't sleep so I thought I'd come and annoy you." John responded with a trace of a grin. He enjoyed spending time with Rodney, he didn't have to worry about what he said, after all McKay hated Meyer as much as he himself did.

"You've been having problems sleeping for longer than this Emily thing haven't you? Since Elizabeth if I'm not mistaken." The air of nonchalance with which McKay said this would have made Sheppard hit any other man, but he knew it was said to disguise Rodney's own painful feelings.

"Yeah, but it's worse in a way now, I used to see her you know, but now it's Em, I guess you heard about the infirmary incident?"

"Everyone heard about the infirmary incident," McKay answered, "I miss Em too you know, it's odd, with her it's kind of worse, she's still alive somewhere. I take it there's no news?" He asked hopefully.

"Nothing, it's been six weeks, and that whole planet has been scanned, Jumpers have covered every continent, the only living things there are of the plant variety." John responded dejectedly. "She isn't there."

"It wasn't your fault you know, if anything it was mine."

"Ok, I know you have a big ego Rodney, but how do take the blame for this one? You weren't even on the team!"

"Exactly. If I had been then she wouldn't have been there, thus she couldn't have been taken."

"But if Meyer hadn't reassigned you, you would have been there, so technically it's her fault." John countered, "Anyway, as a matter of interest, is it possible to receive transmissions when the gate is shut down?"

"Theoretically yes, but it would have to be bounced off several satellites, spaced equally between…" McKay began before he stopped and started to randomly type into his computer.

"Er, Rodney?"

"Shhhh! Concentrating!" After typing for several minutes he sat back with a grin on his face. "You weren't talking about the she-demon upstairs by any chance?"

"Well yeah but..."

"Well she's been receiving a lot of traffic about this time every week since she started, it's a secure channel that I don't recognise, and it's definitely not the SGC she's talking to, there's always an open wormhole for that. No this is coming from somewhere else." He began typing again, and John knowing better this time kept his mouth shut.

McKay started muttering under his breath, "Stupid, slow computers" seemed to be the main gist. Pushing off from his desk he grabbed cable and another laptop, deftly linking them together he started to type swiftly into one whilst waiting for a programme to load on another. After several minutes both computers were displaying a confusing amount of information. "What are you up to?" He muttered.

"What? Nothing!" Replied John dropping the stone he was playing with back onto the desk.

"Not you. But don't touch anything. No her, look." He turned the computers so that Sheppard could see the screens. The left screen showed a list of what appeared to be coordinates, most in black, but several in red, the right hand screen showed a complicated network of dots and lines stretched over what appeared to be a star map.

"So er, what am I looking at?"

"This here, is Earth," Rodney began, pointing at a dot in the bottom right corner of the map screen, "And this, is us." He pointed to the corner diagonally across from Earth. "These lines show the signal, the white lines, ignore them, they don't go anywhere, but the red lines, that's the path of the signal, and they correspond with the red coordinates here, these are points where the signal is boosted, so they must be ships or beacons of some sort, now if I'm right someone's gone to a lot of trouble to hide this signal, you see how they criss-cross? And bounce back to previous points? It's all done to try and confuse the computers, it's a good job I'm not a computer." He sat looking smug for a second before a strange look came across his face.

"Rodney? What's wrong?"

"The signal, it originates form Earth right? But it's not the SGC and the IOA don't have the technology to do this, nor do they have a reason."

"AND?" John prompted, knowing there was more to come from the man

"And, there aren't that many other people with access to this type of stuff, and even less can have ships and outposts stretched other such a large area. I think we need to consider that our 'leader' may be working for someone else."

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