Chapter 5: Stargate Command

John stepped through the gate into the SGC – Stargate Command, Cheyenne Mountain, Colorado – with little fanfare. The guards on duty saluted him as he walked down the ramp, but he was glad that for once, there wasn't more of a welcoming committee.

"Colonel Sheppard, welcome back to Earth, sir. If you'll follow me." A Staff Sergeant – Mackenzie, according to his name badge – motioned John toward the bulkhead doors leading out of the gateroom.

No fanfare whatsoever. He could get used to this. John slung his duffel over his shoulder and followed the sergeant out into the corridors.

"General Mitchell sends his greetings and apologizes he couldn't be here. He was called into an emergency meeting with the IOA earlier this morning." Sergeant Mackenzie led him into a elevator and pressed the button for level 25. "Current time is 0400 hours, Tuesday October 13. Your schedule is in your quarters."

John resisted the urge to let his shoulders slump. They probably could've picked a better time to send him through, but given the differences in day-length between Earth and Atlantis… Twenty-seven and a half hour days was just different enough that gate lag was inevitable on Earth, no matter what time he left.

Four in the morning on Earth was currently mid evening on Atlantis, and it was only going to get worse from there.

"I don't suppose all the important meetings are in the morning?" John asked, hopefully.

Sergeant Mackenzie gave him an odd look. "First IOA meeting is this afternoon."

Perfect. Middle of the night for him.

And Atlantis had been relatively quiet for the past few months, so he had gotten into the habit of actually sleeping through the night for once. Hopefully someone thought to stock him up on stimulants to get through that meeting.

The elevator doors opened out into a similarly drab looking corridor, with only faint markings signifying that they had actually changed levels. John knew the 25th floor had the VIP quarters and since he doubted they were going to let him out of the mountain during this trip, he supposed it was good enough that they gave him decent quarters.

It was only for a couple days. Then it would be up to the wonderful cramped quarters of the Daedalus for the three week trip back to Atlantis.

Hardly glamorous.

Sergeant Mackenzie swiped his badge and opened the door to one of the VIP suites. "Temporary badge is on the side table. Last four is your temporary PIN, but change it when you log in to the laptop." He flipped on the lights, then waved a hand around the room. "Quarters will be accessible to you only. First scheduled appointment is with the NID, regarding the recent attack on Atlantis, at 0900 hours."

John held back a grimace. Though he had nothing in particular against the NID – National Intelligence Department – he wasn't exactly looking forward to being raked over the coals for losing their one good lead on the Trust's infiltration of Atlantis.

Not that that was his fault.

They had had Private Higgins under lock and key.

No one should've been able to get to her.

Dr. Madsen had even checked her over for cyanide pills and the like.

Yet, somehow, Private Higgins had still ended up dead in her cell without sharing one iota of her information.

"Is there anything you need right now, sir?"

John shook himself out of his musing and dropped the duffel onto the floor, glancing around the room. "What floor is the mess, again?"

"Level 22."

"Alright…" He glanced around the room once more, noting the not so subtly placed iron and hanging garment bag. He was going to have to dress up for the IOA, no doubt. "That will be all for now, Sergeant."

He waited until the door shut behind the sergeant, then dropped heavily onto the bed.

It was going to be a long day.

He managed to catch a couple of hours of sleep, then had navigated through the corridors until he successfully found the mess. He had spent a few months in the SGC – when Atlantis had been stolen from them – and had learned his way around. But there was something distinctly lacking about a base not having transporters, automatically opening doors, and interactive maps he could control with his mind. Not to mention that the base was underneath a mountain and he was never going to see the light of day.

The closest he got to the surface was on level three, in a small little meeting room where he was supposed to be meeting the NID agent. It didn't look much bigger than a closet, but for some reason no one seemed keen on letting the NID agent further into the mountain.

John resisted the urge to kick his feet up onto the table and lean back in his chair as he waited.

Because they were making him wait.

The agent was already ten minutes late.

He could've gone all the way up to the entrance to the mountain – seen some sunshine – then made it back here before the agent arrived.

There was a rapid knock on the door and a man in a sharp suit entered the room. He could've given Woolsey a run for his money.

"Colonel Sheppard, it's good to see you again."

John squinted at the man. "Agent… Barrett?" They had crossed paths once, when Jeannie – Rodney's sister – had been kidnapped. Perhaps he was the only NID agent the SGC actually trusted… Everyone knew General O'Neill was a paranoid bastard, after all.

Agent Barrett slid into the chair and slid a cup of coffee across the table. "The guards at the entrance didn't want to let this through." He took a sip of his own cup. "Figured it was the least I could do since I know your time zone is going to be a little off."

John took it gratefully and took a bitter swallow. He was probably going to drink enough coffee over the next couple of days to put Rodney to shame. Not that he was planning to return to Atlantis without at least a ten pound bag of the finest coffee he could get his hands on.

A peace offering for not attempting to bring more zats back to the city.

The agent spread out a couple of file folders on the table, filled with pictures and reports that were painfully familiar to John. Private Higgins, by all accounts, had been well regarded and highly efficient in her work with supply administration. She had spent nearly two years working in the SGC before transferring to Atlantis when the city returned to Pegasus. She had only traveled off world twice since then, but had been good at her job.

No one had expected her to go rogue.

But that was probably the point.

"Private Loretta Higgins, supply administration and operations specialist. She was coming to the end of her twelve-month tour, and just… attacks the commanding officer?" Agent Barrett tapped the last picture they had of her, looking defiant in the brig. "Then manages to commit suicide while under full time guard?"

John grimaced. It didn't look good. "Our CMO examined Private Higgins herself and there was nothing Higgins could use to harm herself. Six hours later…" He trailed off. Higgins had just collapsed. Dead. Autopsy had revealed a fast-acting poison, but no clues to how Higgins had gotten access to it.

"Were you familiar with Private Higgins?"

"As much as a commanding officer can be aware of all his subordinates." And since there was probably only a dozen or so female Marines in the city, he could put names to faces very easily. "She was under Lieutenant Simmons and Sergeant Pilkes. Never had any complaints."

"Simmons is the Navy officer."

"Yes." It had been an olive branch to the other services – army was still waiting their turn to get onto Atlantis. Lieutenant Simmons had been fast-tracked out of the academy and into Atlantis after only a handful of months at the SGC. Though he was greener than green, he had been a good leader and organizer so far. And was without a doubt unaffiliated with the Trust. Rodney had seen to it.

"What about Private Higgins' close contacts? Unit mates?"

John nodded at the stacks of interviews and papers he had brought through with him. "Nothing notable in regards to her job duties. But… she had withdrawn from social activities over the past month and had been visiting Dr. Madsen in the infirmary for migraines."

And even that wasn't considered odd on Atlantis.

Until Higgins had apparently hit a point where the facade couldn't be kept up any longer.

"And her purpose in kidnapping you?"

John snorted. "You'll have to ask someone else about that. In case you didn't read the reports, I was unconscious for all of it."

"Yes, the…" Agent Barrett flipped through the pages of the reports, until he landed on the page that held a picture of the confiscated zat. "Zat 2.0."

Trust Rodney to go trying to rename things.

"Dr. McKay was very unclear on what these modifications mean." Agent Barrett frowned, running a finger down a column of text. "And how such a device made it from Area 51 to Atlantis."

John grit his teeth. "You'll have to ask the Trust that."

Because Rodney and Zelenka had agreed that there was no way Private Higgins had smuggled the device into the city without help. Which meant that someone else was cooperating with the Trust.

"You suspect the Trust has infiltrated Atlantis?" Agent Barrett looked skeptical.

John just shrugged casually. "Who knows. If this is any sign though, we won't know until they reveal themselves." He had a short list of suspects, but he wasn't about to share that with the NID. The last thing he needed was them inviting themselves into his city for an investigation. The IOA would see that for the opportunity it was and jump on it.

And then the city would be completely overrun in bureaucratic nonsense – giving the Trust the perfect opening to kill them all.

Was he being a little dramatic? Maybe…

But if there was one thing General O'Neill had inadvertently taught him, it was that keeping the IOA, the NID, and all other alphabet agencies out of Atlantis was top priority.

Agent Barrett gazed at John for a long moment, before shuffling the folders back together. "Well, we'll keep you appraised of what we find. The Trust has been targeting the IOA, so that's been the focus recently. If there are any links between Private Higgins and the Trust, I'm sure we'll know soon."

John just gave a bland smile, before sipping at his drink once more. He highly doubted he would hear anything more on the Higgins case, unless his own people turned up something. It would get shoved under a rug and categorized as a Pegasus Anomaly.

A cellphone rang.

Agent Barrett pulled a small flip phone out of his pocket, frowned at the number, and answered. "Malcolm." His lips set into an unhappy line at whatever the person on the other end was telling him. "Fine. Search the facility – discretely. And get those tapes." He snapped the phone shut, looking truly annoyed.

"Bad news?" John asked, leaning back in his chair and taking another sip. He was more than happy to have an end to the interrogation.

"A… person of interest dropped off our surveillance." Agent Barrett stacked the folders and pushed back from the table. "If you'll excuse me, I'm going to need to do some damage control."

John waved him out of the room and took the final sip of his coffee.

Altogether, not too painful.

And hopefully, he had at least diverted the NID's interest in Atlantis for the time being.

He could only hope.

Morning was better than evening, as far as John was concerned. Unfortunately, the IOA had decided to schedule all late-afternoon meetings, meaning John was about as sleep deprived as possible. Which they tried to use to their advantage to wrangle an acceptance of foreign-appointed military officers out of him.

He was tired, but not stupid.

More than one country's representative had approached him at the end of the first day of meetings, trying to convince him to take on a contingent of their own specially picked officers. They all well knew Atlantis didn't need more officers, but that didn't matter.

There were more than a few ruffled feathers over Woolsey's special appointee – a British ex-spook, who just happened to be a package deal with a SAS team. Everyone wanted their own country's appointees to make it into the command structure of Atlantis. Never mind the fact that Woolsey was technically an IOA appointee in the first place.

John had almost gleefully referred several representatives to take up their case with Woolsey, especially when it became clear that some of them wanted to use Atlantis as an exotic resort. They didn't quite seem to get that the Pegasus galaxy was still a dangerous place to live. Though the wraith were less of a threat than they had been two years ago, they were still there.

Still waiting to suck the life out of any humans they crossed paths with.

Funny that.

Now, though, he could do what he had actually come back to Earth to do.

John leaned against the railing, looking down on the recruits training on the ground level. Most of the enlisted personnel were unaware he was in the base in the first place, much less that he was secretly vetting them to serve in Atlantis. He had a stack of at least fifty personnel files in his quarters to go over before the next evening.

Sure, people had seen him around the base. A few had even seen him rushing into the IOA meetings in full dress. But unlike all of SG-1, he wasn't likely to be recognized – especially since his return to Earth hadn't been advertised. Aside from his few months serving in the mountain, many had no idea just who Colonel John Sheppard was outside of the mission reports that filtered back.

For once, it was working to his advantage.

"See anything you like?"

Of course, Mitchell showing up was going to blow his cover, because everyone knew who the General was.

John snorted. "You've got a couple that look like they're fresh out of boot." He nodded toward the pair that were carefully sparring, going no further than the locks and bars that had been drilled into every recruit at one point in time.

"Ah, Finstock and Rogers." Mitchell nodded knowingly. "They've yet to go through the Jaffa version of boot camp. They've got excellent marksmanship skills, but are lacking in hand to hand. The Free Jaffa will whip them into shape in no time though."

John crossed his arms across his chest, before turning away from the recruits. He cast a glance at Mitchell, who was dressed up in his field uniform. "Heading out?" It was surprising that the general of the base still went off world, but scuttlebutt was that it had been a condition of him accepting the promotion. It wasn't exactly like there was a whole lot of precedent to undo and it was good practice for his second in command to run the place for a short while.

"Jackson wanted to visit P3X-482 – ruins talking about an ancient warrior race." Mitchell shoved his hands in his pockets, looking almost resigned. "It's been a couple months since I went off planet and Jackson is a trouble magnet, so…"

He had heard stories. There were times it seemed that Rodney was a trouble magnet, but that clearly paled in comparison to Dr. Jackson. The man had been declared dead multiple times. There was a standing order that a funeral couldn't be held until at least eighteen months after his presumed death.

"Colonel Stadler just returned from a raid, so he'll keep things under control here. Should be back by nightfall." Mitchell grinned. "Drinks at mine tonight?"

John blew out a long breath. "Definitely." Maybe he would get out from underneath the mountain, after all. "Have to sit through the IOA meeting this afternoon yet."

Mitchell clapped him on the shoulder, before turning to walk away. "Your SAS team and Woolsey's spook will be back on base tomorrow, so try not to get into too much trouble. I'd hate to have to keep them."

John chuckled. From the sound of the reports, keeping the SAS team would be hardly an inconvenience. The spook on the other hand… John still wasn't quite sure what to make of the man who would likely one day replace Woolsey. Hopefully far in the future.

At least Woolsey was thinking ahead. And having a second in command would allow Woolsey to take a day or two off. To see the galaxy, without putting all the pressure on the department heads. Rodney certainly abhorred the days someone put him in charge of everything.

It made John very glad for Major Lorne – and the fact that Lorne dealt with all his paperwork.

John turned back to the recruits on the main floor and started picking out the ones that might just make the cut. In six months. But that was the entire point of this – to make sure that they got stuck with quality troops and not just those riding out a tour. And the one recruit who had zeroed in on him within five minutes of being on the balcony got full points for situational awareness.

Now it was just a matter of time to see how the others would stack up.

Clawing his eyes out would be preferable to being stuck in this meeting.

IOA representatives were all the same – carefully backstabbing each other so that they might have a slightly more elevated position in potential Atlantis politics.

And none of them were happy about the team selected for the international cooperation agreement – with the exception of the UK representative.

"Perhaps it would be wise to remind you, Mr. Sheppard—"

"Colonel." He had corrected them multiple times. The Chinese representative either didn't care, or was deliberately taking stabs at his status. Either way just made him grit his teeth even harder.

"Excuse me, Colonel Sheppard, but would it not be more beneficial for the technological advances to be studied through international cooperation, rather than remain all within the sphere of Atlantis?"

It took him a moment to parse through the gibberish and stared at her. "You're asking me, the military commander, if I think technology should be brought back to Earth for study? First of all, you'd be better off asking the Head of Science – but I know none of you want to deal with McKay. Secondly, Atlantis is already an example of international cooperation, in that we have scientists from twenty-three different countries working to identify the most important discoveries. Thirdly, do you understand at all what you're asking? You don't want us to identify possible contaminants, exploding machinery, and biohazards before we share our discoveries? May I remind you that that was how we lost our CMO in the third year."

He might have been channeling Rodney just a little bit.

"What Colonel Sheppard is trying to say is that technological advances that are deemed safe are brought back to Earth." Mr. Callow, the American representative, cut a glance in John's direction, as if asking him to just shut up.

John wasn't exactly sure how he was supposed to do that when he was being asked a direct question. It wasn't like he wanted to be in these meetings in the first place.

"Yes, and distance to Atlantis is so far that it takes months before those return to Earth, and months more before your government decides that those technologies are safe to share with the rest of the world." The Chinese representative seemed particularly insistent on this point. "It would be better for Atlantis to be nearby to share in discoveries."

"And weaponry," the French representative cut in, looking particularly serious. "The Ori fleets are still threats – why leave our best weapon in another galaxy?"

John swallowed down the immediate retort, but it was the same song and dance every time. Two or three countries campaigned passionately that Atlantis was far more useful on Earth than protecting another galaxy. Never mind that in protecting another galaxy from the wraith, they were doing their best to make sure that the wraith never tried to make another run on Earth… Other countries were campaigning passionately that Atlantis should be their own personal bolt hole when the latest galactic threat came to Earth and were trying their hardest to make sure that their people were positioned to aid their country the most.

Any hope at making forward momentum was lost, as the meeting devolved into bickering.

And no one mentioned the elephant in the room that was the Trust and the recent infiltration attempts.

John settled back in his chair, just waiting until the next argument picked up. Something would be relevant, eventually.

A/N: Apologies for taking so long. This was supposed to be posted a week ago, but nearly everything that could have gone wrong in the past two weeks, has gone wrong. I'm not going to make any promises on posting schedule, but I am trying for once a week. Anyway. Thoughts? For those of you unfamiliar with John Sheppard, what do you think? Alex is as much in the dark about many things as the rest of you all, so things will be explained as we go.