Chapter 2
"Colonel, you're just in time." Col. Carter smiled at Sheppard as he walked into the operations area then nodded at Chuck. "Dial the Gate, please."
"Yes, Ma'am." The technician began pressing the symbols on the console. Seconds later, the wormhole opened. They waited, knowing the SGC was going through the same process. After several minutes, he said, "We're through to Midway, Colonel."
"Midway, this is Atlantis. Do you copy?"
A disembodied male voice replied. "Atlantis, this is Midway. We're waiting for the SGC to dial in, too."
Having both planets dial in at once wasn't an unusual procedure. As was the case tonight, sometimes there was a transfer of personnel and supplies. Tonight, a handful of personnel were returning to Earth after their stints in Pegasus. Since they needed to spend 24 hours on Midway, there was no need for the wormhole to go all the way to the Milky Way. The station, in turn, was getting a delivery of food and equipment from Earth.
"Good to hear. How are things going there?" Sam was happy the bridge to Earth was working as well as they all hoped. Not needing the ZPM for the long journey or to keep in regular contact with the SGC was more than valuable.
"Fine, thank you, Colonel." The voice replied. "We have a wormhole coming in from the Milky Way now."
A few minutes later, the departing personnel disappeared through the event horizon. The data transfer was lightening fast.
"We'll dial in as soon as we're on line again. It shouldn't be more than a couple of hours."
"We copy, Colonel. Good luck."
"Thank you. Atlantis out." With that, the Gate shut down. "Apollo, we're taking the Gate offline."
Ellis responded. "Acknowledged."
Col. Carter turned to McKay. "Rodney, you can run the program now."
"Finally." He muttered with annoyance. He snapped his fingers several times at the people around him then hunched over his computer and began typing commands. Sitting nearby, Zelenka was also typing furiously, occasionally glancing at McKay. Two minutes later, McKay looked up at the two Colonels. "I'm ready."
Sam slipped into a chair at one of the computers and nodded her head. "Okay, let's do it."
McKay turned to his laptop. "Right. Taking the Gate offline in three, two, one." With great exaggeration, he pressed a key on the console next to his laptop. Everyone looked around in expectation, and back at him when nothing happened. "Well, what did you expect, fireworks?"
Without another glance around, the chief scientist began entering more commands into his laptop. Sam on one side with Radek and nearly a dozen technicians on consoles and laptops around them peered at monitors and screens, closely watching the installation and functions of the city's systems.
Sheppard, a vague uneasiness nagging at him, decided to stay in the vicinity. He watched McKay's computer screen and the Ancient monitors as work progressed. Occasionally, he would stop by during such a project, but today's undivided attention was unusual. Twenty minutes into the process, McKay turned and glared at him. "Is there a problem?"
"No." John glanced at him then back at the screen. After a moment, he turned and walked away.
Sam, observing the exchange out of the corner of her eye, was tempted to ask her 2IC what was worrying him, but decided against it. Having the Gate offline for even a minute was a little scary for everyone.
Slightly more than two hours later, McKay dialed the Gate. The address he input started the macro sequence that would connect them to the Midway station. Everyone in the Gate room held their breath until the wormhole was established, but they only relaxed later, when the technician on Midway dialed Atlantis, confirming the system was online and fully functioning in both directions.
No-one seemed to notice Sheppard disappear down the stairs at the far side of the control room deck.
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"This is ridiculous." Sheppard grumbled as he got up. It was the third night in a row he'd woken with the distinct impression something was out of place. He glanced at his watch. 0217 "What the hell is going on?"
He picked up the radio and turned up the volume. Tonight, he'd left it within easy reach. After listening to the various frequencies used in the city for several minutes, John decided that all was safe and quiet. He also decided that maybe Carter was right. They all needed a break.
Instead of turning the radio off John turned the sound down to just audible again and put it back on the cabinet next to the bed. He rolled onto his back and took several long, deep breaths, trying to dispel the unsettling feeling that persisted. After fifteen minutes, he got up, dressed and left his quarters. The only way he was going to get more sleep tonight was to take a quick look around.
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Col. Carter disliked the necessity of conducting meetings with her chief medical officer and the base psychologist. She understood the need to keep a close watch on the physical and mental health of the people under her command. They were in a galaxy millions of light years from home with only a couple of ships and a small bridge connecting them with help. Those facts did not make the briefings any more palatable.
She smiled at Jennifer Keller and the interim replacement for Kate Heightmeyer, Beth Reynolds. Dr. Reynolds was quite different to Kate. She was tall and big boned with graying red hair, and had a warm, straightforward demeanor. The contrast to the lost psychologist was both disconcerting and welcome. They did not need daily reminders of their friend.
Beth came fully briefed about the unique situation in Pegasus. She had been consulting with the SGC on personnel that would be suitable for deployment here, so she was familiar with the files of current and past expedition members and all mission reports. She'd also been a friend of Kate Heightmeyer, so she understood the impact of her death. Beth would remain on Atlantis until a more permanent replacement was found and brought up to speed.
The Atlantis commander looked at Jennifer. "How are things in the infirmary?"
She took a deep breath before speaking. "Apart from a broken arm and some bruises and scrapes from recent missions, the worst case I have right now is an emergency appendectomy."
"Appendectomy?" Sam raised an eyebrow.
"Sgt. Turner." Jennifer responded. "The surgery was last night, and he's already up and around."
"Nothing else?" Sam felt there was something more.
A slight frown creased Jennifer's brow. "There have been a few more cases of minor illnesses than normal, some signs of sleeplessness and loss of appetite. I'm keeping a close eye on it, but I'm sure it's nothing serious. I think we're all just a little tired." The frown disappeared. "The time off you ordered will give everyone some breathing room."
"I thought it might help." Sam turned to the psychologist. "Have you seen anything we should be concerned about?"
"The critical incident stress debriefings are going well." Dr. Reynolds barely glanced at the data pad on her lap. She brought it out of habit even though she knew all of the information it contained. "There are some signs of stress, and a few people could use a couple of weeks back on Earth, but most are quite doing well. Better than one might expect, actually."
Sam nodded. "A lot of that is due to you and Kate. It's also a pretty tight-knit group. Most of them were stationed at the SGC before coming here, which helped them understand what to expect."
"Thank you, Colonel." Beth acknowledged the validation of her contribution. "Having good commanders and support on the ground has a lot to do with it, too."
"I inherited a good team." Sam said with sincerity. "You'll keep me informed of any concerns you have?"
"Definitely. I'm preparing a complete report for you. I'll email it later today." Beth said as she and Jennifer stood up. She didn't move, though. Piercing eyes studied the colonel's face. "What about you? When will you get a few days off?"
The question caught Sam by surprise. "Um, well, soon."
"Yes, Colonel. Soon." Dr. Reynolds said with an unreadable expression, as she and Jennifer turned to leave the office.
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Maj. Lorne waited patiently for his commanding officer. He knew Sheppard was supposed to be relaxing for a few days, but apparently the lieutenant colonel thought differently. Instead, he was sitting at a computer in one of the labs doing…something. Evan caught a glimpse of what he thought were schematics of the south pier of the city.
"Colonel?"
Sheppard blinked, suddenly realizing that he was waiting. "Sorry. I want everyone with the gene to get in at least six hours of flight time, including two hours flying formations with three other Jumpers. They also need a couple of hours in battle simulations."
"Sir?" Lorne wasn't sure where this was coming from. All Air Force and Marine personnel with the Ancient gene were thoroughly trained on the Jumpers as soon as they came to Atlantis. Civilians, however, were generally given an hour or two of practice, just enough to enable them to get from point A to point B without crashing.
"After what happened in the asteroid field, I want to be sure everyone on this base has half a chance of protecting Atlantis if we're ever cut off again." Sheppard replied firmly. "After the initial training, everyone is to have at least an hour flying a Jumper once a month."
Reasonable enough, Lorne thought, even though it was highly unlikely that Atlantis would be caught so short on pilots again. He was more curious about the colonel's sudden need to beef up the already more than adequate security of the city. This was the third order in three days he'd come up with. First, he increased the number of graveyard watch patrols by one quarter. Yesterday, he pulled a spot inspection of the armories, a first, and decided they needed more heavy small arms near the Gate room.
"Yes, Sir. I'll have a schedule for your review tomorrow."
"Thanks."
The major left Sheppard completely engrossed in studying the schematics. He frowned deeply as he walked down the corridor. Everything was entirely reasonable considering the chaos and loss of recent months. Why did it feel that it just wasn't quite right?
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Beth Reynolds' office was near the one that had been used by Kate Heightmeyer, but different in layout and décor. Beth scavenged the most comfortable chairs and sofa she could find in the city and arranged them almost as a sitting room. Even though her stay on Atlantis would be relatively brief, she brought some of the comforts of home. Colorful pillows and a large Persian rug added warmth to the room's neutral tones.
She sat on the sofa, her laptop sitting on a well used wooden lap desk resting on her knees. The file notes she was typing were momentarily forgotten as she stared at the door. John Sheppard had been the last appointment of the day. She knew him from interviews conducted four years previously at the SGC, and more recently during the brief return of the Ancients to Atlantis. Everyone working on the Stargate project on Earth was thoroughly vetted. Even though danger and death were experienced by military personnel on Earth every day, the added secrecy and utter strangeness of the work at the SGC required more of every individual involved. Personnel sent to the Pegasus Galaxy needed to be on a level of their own.
Sheppard was unceremoniously dropped into their weird little universe without any warning. Going from the snug, safe mindset of being the only intelligent life forms anywhere to Stargates and aliens and hyperspace was usually afforded time and preparation. They'd all been concerned about his reaction to it, some more so than others. He surprised even her, though, and took to it like he was born to do it, spending the few short weeks before the expedition left absorbing everything thrown at him. At the same time, Sheppard spent as much time as possible in the chair at the Antarctic outpost, pulling enough information out of the Ancient database to keep the scientists busy for months or years.
The two meetings Beth had with him since arriving and Kate's file notes only reinforced her initial assessment of Col. Sheppard. He had a rock solid core that allowed him to keep functioning at an extraordinarily high level no matter what the circumstances. He did it with a deceptively laidback demeanor. But, now, for the first time, Beth was worried.
She knew that, despite the face he showed the world, John felt things deeply. It fueled his need to protect people. She was certain recent events would have shaken him. He thought he was directly responsible for Kate's death and, to a large degree, the losses of Elizabeth and Carson. Add to that his hand in the circumstances of Wallace's death at the SGC and the vicious rampage of the Replicators and Wraith on the humans in Pegasus, and the load was crushing.
Even if reserved when it came to giving details about himself, his feelings, thoughts or past, John was a relaxed individual. This evening, however, the discussion was very different. His normally charming, yet thoughtful, manner was missing. He was tense and distracted. Her gentle questioning received only, "I'm fine" as a response.
Beth blinked and looked down at the laptop. It was in sleep mode. She logged in again and read the last entry. It was about a discussion with Sam Carter earlier in the day. The colonel was concerned with the perceptible change in Sheppard since his return from the search and rescue mission on M7R-829.
The psychologist thought about it for a long time before adding a final few sentences and logging off again. He was the last person in either galaxy she thought might lose his way but a fear of the cumulative effect of the brainwashing, for want of a better word, and the events of the last few months was beginning to take root.
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"This is the second time in three days." Ronon growled. He'd waited as long as he could, which wasn't very long at all. He stopped prowling around the workout room and looked at Teyla, who sat on the bench against the window. "You hungry?"
She was, actually. The baby growing inside her made her almost constantly hungry. "Are you sure he agreed to spar today?"
"Yes, I'm sure." He helped her up. "I don't know what's going on, but he's acting kind of…"
"Distracted?" Teyla finished as they left the room.
"I was going to say weird. Haven't you noticed?"
She sighed. "I have hardly seen John since you returned from the last mission. However, I agree. He did seem quite preoccupied when I spoke with him earlier today."
"Do you know what's going on?" They stepped into a transporter.
Teyla responded as they exited near the mess hall. "I only know that he has been busy implementing new security measures in the city."
Ronon grunted. "He's supposed to be standing down for a few days. Carter ordered it."
"I know. He may just be taking the opportunity to increase security." She said even though she was not convinced.
"It's more than that. He's jumpy, worried about something."
"Jumpy?" She glanced up at him quizzically. That was not a word she would normally associate with John. "Have you asked him about it?"
"Yeah. He dodged the question."
"I will try to talk with him." The entered the mess hall.
"Good luck." He was skeptical. They both knew it was highly unlikely she'd get an answer.
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The vague feeling that he was waiting for another shoe to drop nagged at the edge of his mind and would not go away.
Sheppard stood at the window in his quarters. It was still more than two hours until sunrise and the world was dark. He missed the spectacular starscape on Lantea. The perfect clear skies, unpolluted with light and smog like Earth, was breathtaking. Even after three years, he hadn't tired of it. This new planet was equally unpolluted, but had a very different perspective of the galaxy. It was still impressive, just not quite as much as their previous home. At least so far, the view was also obstructed by clouds more often than not. He'd have to wait through a full year before passing final judgment.
He rubbed his right temple in hopes of easing the ache that had been there for days as he walked back to his desk, sat down and checked the city's defense plans one more time. Short of having a full complement of ZPMs, a couple more battalions of Marines, rail guns on every other balcony and several of the new Asgard plasma beam weapons, there was nothing else he could do to protect the city from attack. Training a back-up or two for the weapons chair might help, but there weren't enough drones or the power to waste, and no-one would come close to his accuracy. His innate ability to use the Ancient technology was unique. Being special was sometimes a royal pain in the ass.
With a deep sigh, John shut down the computer and went back to bed. He needed a little more sleep before meeting Ronon for the sparring session he'd promised the last couple of days. He was going to pay dearly for ditching him twice in a row. The Satedan was not particularly happy with him.
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McKay sat down at one of the computers in the control center, a coffee mug in his left hand. The diagnostic program that had been running for a couple of hours was nearly finished. Some kind of minor error in the city's operating system appeared two days ago, causing a few intermittent shutdowns in non-essential functions. Of course, it was nothing to do with the streamlining program he loaded three days before that. The Gate worked perfectly when they dialed earth every day since, as well as when Earth dialed in. He sipped coffee as he watched the results begin to scroll by on the monitor.
Without warning, the consoles around him went down. Glaring at the technician sitting nearby, he demanded, "What did you do?"
The young man frowned at the controls then looked at him. He held up both hands. "Nothing, Sir. I didn't touch anything."
The astrophysicist spun around, looking at everyone in the control room in turn. Every Ancient console and screen was dark. They all shook their heads, hands up in denial of wrongdoing. He turned back to his laptop and started typing rapidly.
"Dr. McKay?" The technician watched him, not knowing what to do.
"What? Can't you see I'm…" He stopped typing and stared at the screen. "No-one touch anything!"
Col. Carter came out of her office. Only light from the late afternoon sun and the minimal emergency lighting illuminated the space. "Rodney? What's going on?"
His eyes remained on the screen, watching data scroll by too rapidly to read. "I don't know. I was just running diagnostics to determine what's been causing the malfunctions."
"Are we in lockdown again, Doctor?" One of the other technicians asked.
McKay shook his head as he kept typing. "No. No. I…I don't think so. It's almost as if…" He reached out and placed his hand on one of the ATA pads. The control keys glowed momentarily then darkened again. He pressed harder and stared at it, trying to will it into life. It came online. With a loud exhale, Rodney took his hand away, only to see the controls go dead again.
Sam looked at one of the technicians she knew had the ancient gene. "Try that one."
The young man took a deep breath and put his hand on the pad. It came to life for barely a second even though he kept his hand on the pad. He closed his eyes in concentration, but it remained inactive.
"Rodney?" Sam walked around and sat at another laptop.
"It's the city's operating system. Something's wrong." He added before anyone could ask, "No, I don't know why and I'm working on it."
"Okay. We'll figure it out." She fervently hoped it was a very temporary glitch and that everything would be up and running again in a few minutes. As those minutes ticked by, though, Atlantis' commander and chief scientist grew certain that it was far more serious than an easily fixed glitch. "Could it be a problem with the ZPM?"
"No, no. The ZedPM is fine. We have plenty of power." He stopped typing to point at a graph on the screen. "This was just before everything shut down."
A few minutes later, a Marine lieutenant approached. She touched the transceiver in her left ear. "Col. Carter, we're getting a lot of radio traffic on the emergency channel. It looks like the Ancient systems are down all over the city."
"Thank you, Lieutenant." Sam barely glanced up from the laptop. "Tell them we're working on it. Unless there's an emergency, everyone should just sit tight for now."
"Wait, wait." McKay snapped his fingers. "We need to find out if anything in the city that needs the Ancient gene is working."
"Can we use the city wide comms?" Sam asked as she turned to Chuck. "Try it."
The technician pressed the control, but nothing happened. He tried again, and shook his head.
"McKay, this is Sheppard." The colonel's voice sounded in their transceivers.
McKay tapped his transceiver. "Yes, I know. There's a problem."
"What kind of problem? What's going on?" It was obvious Sheppard was not happy.
"I don't know, exactly. It looks like the Ancient technology is offline."
"I know that. Is it another lockdown?"
"No. It's not a lockdown. We obviously have communications and it looks like none of the doors are locked." McKay continued pounding on the keyboard as he spoke. "Look, I don't have time to talk right now.
"Where are you, John?" Col. Carter asked.
"Out on the south pier. You're in the control room, I take it?"
"Yes. We're trying to determine what happened." She responded.
McKay placed his hand on the ATA pad again. This time, nothing happened. He muttered under his breath then spoke aloud into his comm. "I…we need you up here. Now."
"In a minute." Sheppard spoke again. "Colonel, we should be on alert."
"You read my mind." She responded.
"Maj. Lorne, all command personnel, go to channel four." There was a chorus of "Yes, Sirs". Col. Carter knew that her second in command was implementing the emergency plans for safeguarding the city. A minute later, Sheppard spoke again. "Colonel, I'm sending up reinforcements to secure the Gate room."
Almost immediately, two squads of Marines took up positions around the Gate. Minutes later, even more Marines appeared, carrying weapons ranging from P-90s to heavy machine guns. Knowing full well that the iris was also offline, everyone in the control area breathed a small sigh of relief at the added protection.
