Authors Note: So this is the first non AU I've written in a long time but the idea wouldn't leave me alone. I hope you all enjoy it, please read and review, let me know what you think!

Chapter 1

John Sheppard wrung his hands together as he sat on the hard metal chair and waited. He wasn't sure how long he'd already been sitting there for but it felt like an eternity. He couldn't move though, couldn't leave until he knew what was happening beyond the doors in front of him, he needed to know. The infirmary was quiet, he imagined most of the city seemed quieter than usual as people waited to hear what was going on.

John thought back over the last few months, to try and pinpoint exactly where things had gone so wrong, how they'd ended up where they were now. The radio informed him he was required in the briefing room, he sighed, looking at the doors, he couldn't leave again, not yet.

He clicked his radio, knowing it was the wrong thing but he needed to be here, "I'll be there shortly."

"John," a voice came from his side, he saw Teyla standing there, worry in her eyes. He was usually better at being aware of his environment but he hadn't even heard her approach. "You need to go."

"I can't," he replied, looking once again at the doors.

"I will remain here. If anything happens I will radio you at once," she told him, her worry giving way momentarily to determination. "You must go."

She was right, he didn't like it, but she was right. He stood up, not taking his eyes off the door. "The moment you know something…"

"You'll know it," Teyla finished for him with a slight nod of her head.

He left reluctantly, Teyla would be as good as her word. He made his way through the city, it was as quiet as he'd been expecting. It was like Atlantis itself was holding its breath, waiting, wondering what would happen next.

He arrived at the briefing room which had been set up as a temporary office for their latest arrival from Earth. He seemed to have made himself at home, reports were piled up on the table, a dark jacket was slung over the back of a chair. The single occupant of the makeshift office stood as he entered. He'd met Special Agent Damien Gavorn briefly upon his arrival and ordered his people to get him set up in the briefing room with everything he needed.

"Colonel Sheppard, have a seat," he gestured to an empty chair. He waited for John to sit down before taking his own seat again. "I've begun reading the reports, it would seem there's been a great deal of commotion here on Atlantis over the last few months."

"We've had some issues," John replied cautiously, he didn't know what to make of the man yet.

"Yes, well I'm here to determine if one of those issues lead to two of your people ending up dead, one recovering from serious injuries and your leader currently undergoing surgery to try and save her life."

John nodded, keeping his outward reaction to a minimum, it was more difficult than he would have liked, "I know why you're here, our people will cooperate fully with your investigation."

"Good, let's start with you."

"I'm a suspect?" John questioned with a raised eyebrow.

"Everyone is a suspect," Gavorn replied, switching on a recording device. He went through a well-rehearsed introduction for the recording, the day and time, who was present. "Colonel Sheppard, can you take me through your role here on Atlantis?"

"I'm the ranking military officer, I'm the second in command of the city after Dr Weir, I also head up one of the off-world teams," John explained. He bit back his frustration, he didn't have time to be sitting here answering questions Gavorn already knew the answer to.

"You're the ranking military officer, but only the second in command?" Gavorn questioned. "How do you feel about a civilian being in charge?"

"Dr Weir is an excellent leader, I doubt anyone could run this place the way she does," John told him, already annoyed with the line of questioning and knowing where it was going.

"So you get along well?" Gavorn asked.

"Yes."

"Do you always get along well, surely there are times that you disagree with one another?"

"We sometimes disagree on things but we discuss them, we value one another's perspectives, in the end, our differences are what makes us better," John explained. He forced himself to sit back in his chair, to feign a calm he wasn't close to feeling.

"But Dr Weir ultimately makes the decisions."

It was a statement, not a question so John didn't bother to respond. Gavorn made a short humming noise, then typed something into a computer tablet. There was silence in the room for several moments, John suspected it was supposed to make him uncomfortable, it didn't work. The only thing it did was make him feel was more impatient, more restless.

"Do you have any thoughts on who could be behind all of this?" Gavorn asked and the sudden change in direction took John by surprise, that was probably on purpose too.

"I have some thoughts on it."

Gavorn made that short hum again, looking at his tablet. "As I said, a lot has happened here over the last few months, some of it almost definitely contributed to the situation you now find yourselves in. My intention, Colonel, is to piece together the timeline, go through these incidents and determine what happened, it will likely take several interviews."

"Determine away," John told him, eager to get on with the interview so he could leave.

"There was a confrontation a few months ago between Dr McKay and one of the other scientists, the same scientist who would later have another confrontation with Dr Weir. You were there, why don't you tell me what happened that day?"

John thought back, McKay had a lot of confrontations with other members of the science team but he knew which one Gavorn was referring to.

xXx

John walked into the lab where McKay was currently yelling at someone, a young scientist who John had to think for a moment to remember his name, Dr Winters. "Alright, what's going on?" he asked when there was a brief pause in the yelling.

"Dr Winter's activated the device that AR3 brought back yesterday and now Dr Hale is missing," Rodney told him, sending a severe look at Winters who clenched his jaw.

"What do you mean, he's missing?" John questioned as Elizabeth joined them. She moved to stand next to him, raising an eyebrow at Rodney expectantly, her face already filled with concern for one of their people.

"I mean missing," Rodney replied, "As in, we don't know where he is."

"Rodney," Elizabeth admonished.

"He was working in here running some scans on the device so we could gather more information about it before we did something stupid, like turning it on before we knew what it was," Rodney explained, directing some of his statement toward the scientist, Winters stared back, looking more angry than chastised.

"It was an accident," he defended.

"You shouldn't have been touching it in the first place," Rodney replied with obvious annoyance at being interrupted. "The only writing visible on the whole device reads 'danger'. I left instructions for Hale to run the scans and for the device to be left alone until we had a chance to look at the results. This is why."

"Alright, Dr Winters, why don't you tell us what happened?" Elizabeth suggested, it looked like Rodney was going to say something else but a look from Elizabeth quickly silenced him.

Dr Winters glanced at Rodney, his expression almost… gloating. "Dr Hale was running the scans, he said he wasn't picking up any energy signatures from the device, that we might need to power it up before we could get any decent information on what it was. I suggested we take a look at it, to see if we could find a way to get some power going."

"And Hale agreed?" Rodney asked disbelievingly. "That seems unlikely, he's pretty good at following instructions."

"He… didn't agree exactly, he said we should finish the remaining scans and contact you before we tried anything," Winters continued to explain. "I agreed, but I just figured I'd take a quick look, just to see if the device had a built-in power source or if we would need to hook one up. I was just trying to save time later."

"So you touched it?" Rodney exclaimed, "even though you had explicit instructions not to."

"I wasn't trying to turn it on, I didn't do it on purpose, I moved this piece here," Winters told him, moving his hand to point at the device.

"Don't touch it again," Rodney blocked his hand, "Let's not make everyone else disappear."

Winters glared at him, "I wasn't going to. I moved that part, then there was a bright light, I couldn't see for a second, then Hale was gone. I looked for him, I thought maybe he'd left the room when I touched the device but I couldn't find him. We can just undo it, right, bring him back from wherever the device sent him?"

"We have no idea what this device does!" Rodney shouted, "When I leave instructions, I do it for a reason. We don't know that the device didn't just vaporize him, your incompetence might have just cost Hale his life, all because you can't follow a simple instruction."

"That's hardly fair!" Winters shouted back, his face reddening, though whether it was from embarrassment or anger was difficult to tell, maybe both.

"I imagine Hale thinks the same," Rodney countered.

"Alright," John broke up the argument. "We can assign blame later, what do we need to do to figure out what happened to Hale?"

Rodney threw his arms up and shook his head, "I need to go through the scans Hale was doing, then I can examine the device, carefully."

"Then I suggest you get started," Elizabeth said.

xXx

"Hale was rescued," Gavorn stated looking at the report on his tablet. "You were able to find him."

"Dr McKay figured out that the device worked similar to a transporter, we found some information in the Ancient database that Dr Weir was able to translate. The device was a prototype that was meant to be used for transporting cargo. It worked by storing the molecular pattern of objects, you could then carry the device to wherever you wanted to and reconstitute the cargo," John did his best to explain, hoping he'd gotten it right. "It wasn't meant for transporting people, the device was old and damaged so it took some time but we were able to get Hale back. He was kind of out of it for a few days but he did recover."

"How did Dr Winters seem afterwards?"

"He was relieved that we had managed to get Hale back, he apologised to him. We thought that would be the end of it," John told him.

"But it wasn't," Gavorn said, again it was a statement, not a question.

"No, it wasn't."

TBC