Chapter 4

The familiar sound of an incoming wormhole caught them all by surprise. Chuck reached out to raise the shield then froze. "Col. Carter?"

There was no option. Sam just hoped that it activated and that Sheppard could control it. "Raise the shield."

McKay checked the IDC. "It's the Alpha site. They're early."

"What the hell's going on?" Sheppard demanded roughly.

"It's the check-in from the Alpha site, John." Sam replied quickly. "We'll make it fast. Are you okay?"

"Yeah." He grunted breathlessly.

"Atlantis, this is Maj. Owens. Sorry we're a couple of hours early. We're expecting a sizable thunderstorm shortly and didn't want to run the risk of lightening strikes." The apologetic commanding officer at the Alpha site half smiled on the screen.

The Gate at the Alpha site was exposed and the risk was very real, but Sam cringed at the thought of the strain this could be putting on Sheppard. "Major, this is Col. Carter. No problem about the early call, but I'm afraid this has to be brief. We have a virus in the operating system that is causing some problems. What's your status there?"

"Nothing to report, Colonel. We're in good shape." He was obviously concerned but didn't ask for further details. "Anything we can do?"

"Two things. You can suspend daily check in until further notice. Also, contact 621 and let them know the same. If either of you have an emergency, though, dial back in."

"Yes, Ma'am."

"The Apollo is due to be in orbit above Atlantis in a couple of hours. We'll let you know when we have everything sorted out here."

"Good luck, Colonel. Owens out."

The wormhole dissolved.

"John, this is Carter. Are you alright?"

It was a moment before he responded. It was more of a gasp than a word. "Yeah."

She winced. "It's time for a break, anyway. Can you give us a few more minutes to prepare?"

"Sure."

Sam turned to look at Rodney, who was quickly getting ready for the power down. There was no protest this time. The activation of the Gate startled them all, so he was certain it had been very hard for Sheppard to maintain the steady level of control without even a hint of an interruption.

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A pre-dawn glow was just beginning to lighten the sky when the Apollo emerged from hyperspace.

"Atlantis, this is the Apollo."

"Col. Ellis, it's good to hear from you." Even though she'd been kept informed of the ship's progress, Sam was happy the ship arrived. After the Alpha site dialed in a few hours before, she'd been uncertain about having John go back to the chair. They planned to be powered down at the scheduled dial in time, both to make sure it didn't overwhelm him and to see if the Gate would allow the incoming wormhole. Sam agreed reluctantly, but only when he insisted it did nothing more than startle him and he was able to continue.

"We'll be in orbit above you in twelve minutes. Our sensors indicate the city is back online. Can you confirm?"

"Col. Sheppard has been keeping the lights on so that we can determine the extent of the damage and start repairs. It looks like a Trojan Horse was loaded into the city's operating system. We have some scanner capabilities at the moment, but the whole system is so compromised it may be unreliable. We detected a pair of Hive ships on a course that could bring them fairly close to us. Can you keep an eye on them, please? We're sending you the coordinates."

"Be glad to. I'll have a report for you when I beam down."

"Thank you. We'll see you in a few minutes."

"Ellis out." He broke off communications.

"John, did you hear that?" Sam waited for him to respond.

"Yes, Colonel."

"I think we can stop. Can you give us the time until the Apollo arrives? We'll get you and Ronon beamed up once she's in orbit."

As promised, the Apollo assumed orbit within minutes. Department heads were again alerted that the shutdown would occur when the Apollo arrived so, as soon as Ellis radioed he was beaming down, Sheppard was given the all clear.

"Any time, John." Sam confirmed. The city went offline before she said his name.

Meager emergency lights were supplemented by the makeshift lighting set up the previous afternoon. The shadows cast by the harsh lights would soon shift and change with the coming sunlight. A deep sense of the vulnerability of the great city and its inhabitants made Col. Carter shiver.

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The conference room was full. Most department heads arrived on foot, some a little out of breath after climbing several flights of stairs. The Apollo obligingly beamed in anyone working in the more remote parts of the city at the same time as Sheppard and Ronon. The transporters were functioning while he was in the chair, but it was deemed too risky to use them except in the most extreme emergencies.

As a precaution, Col. Carter ordered that no Ancient technology could be used unless it was cleared with her or McKay first. Having the Apollo in orbit now would give them support for almost any emergency that might happen in the city.

Once they were settled, Sam looked at the expedition's quartermaster, Sgt. Williams. He was a small, wiry man, somewhere between forty and sixty years in age. An ability to do his job proven in two long tours of duty in the Middle East made him ideal to keep them fed.

"As you know, we have water. The plumbing seems to be in working order."

Rodney interrupted him. "For some unknown reason, the ventilation and plumbing systems, including hot water, are working. I guess it was overlooked while the viruses were being written."

"Yes, Sir. We have enough supplies on hand for two months, Colonel. We'll be taking a shipment from the Apollo, as well, that will give us another month, easily. Fresh fruit and vegetables will last for the next eight days, so after that it's canned and dried unless we can get to the sources we found on the mainland." The botanists quickly searched for and found several varieties of trees that bore edible, and tasty, fruit on the mainland not long after the city landed on the planet. Two root vegetables were also identified as edible and more were being tested. "There won't be much in the way of hot food until this is sorted out, but we've been there before. We've set up stations in strategic areas so that people don't have to get to the mess hall for meals."

"Thank you, Sergeant." Sam nodded her thanks and permission to leave. She could see he wanted to be out of there. Too much brass in the room.

"Thank you, Colonel." Williams stood and quickly left.

"Col. Ellis, were you able to contact the SGC?"

"Yes, through Midway. They asked if they should send help, but I let them know your concerns about using the Gate until more is known about what happened. General Landry said to let him know if they can do anything."

"Very good." She appreciated Landry's support, even if only in spirit at this time. "What about those Hive ships?"

"It's a fleet of two Hives and four cruisers, with a handful of minor support ships. The course they're on will take them a couple thousand light years away, but we're keeping an eye on them."

"Thank you. That's a lucky break for us." She looked to the CMO next. "Dr. Keller?"

"The infirmary is ready. It looks like all of the equipment there is virus free." Jennifer glanced down at a data tablet on the table in front of her. A state of readiness was the norm here. It was a way of life. "Thanks to the Apollo, we're fully restocked. As you know, we always have sufficient supplies to keep us going for six months if we were cut off from Earth. The only concerns I have are the blood products and some temperature sensitive drugs."

"Does that mean if we need blood…" McKay asked quickly.

"No, no." The doctor held up a hand. "We're fine for a while. The refrigeration units are well insulated and we have them connected to the naquadah generator assigned to the infirmary, so we should be fine. I just wanted to make you aware that we have perishable medical supplies."

"We have a couple of backup naquadah generators on the Apollo, and we can store anything you need." Ellis offered.

"I hope it won't come to that." Sam acknowledged. "Anything else, Doctor?"

Jennifer shook her head slowly. "Well, we have only one in-patient at the moment, but he's in good condition and should be discharged to quarters by tomorrow. Otherwise, it's been fairly quiet."

"Thank you." Next around the table was Lorne. "Major, how are the defense preparations coming?"

"Everything's pretty much in place, Colonel. Personnel are on readiness status, and all weapons and all equipment operational." He glanced a little uncertainly at Sheppard, wondering if the Colonel's sudden preoccupation with the city's defenses was merely a coincidence or something else. "I think we're as ready as we can be."

"Very good." She expected nothing less. Sheppard ran a fairly relaxed military setup here, but he kept his people well trained and prepared for whatever came their way. He led by example, and all too often by risking his own neck. They appreciated it and responded by giving their best. She turned to McKay. "Rodney, can you give us a brief overview of the situation, please?"

He looked up from his laptop. "Someone loaded a Trojan Horse into the operating system, and don't ask me when. Anyway, it released viruses targeting both vital and non-vital functions, including the main operating system, Gate operations, the shield, cloak, transporters, lights, etc. Actually, almost every Ancient function has been affected. And," he threw Sheppard a harsh glance, "as has been suggested, we can't just wipe the whole thing clean and load a back-up. We, meaning me, have to painstakingly go through billions, yes, billions, of code line by line…"

"McKay." John stopped him before he could get going. He wasn't in the mood.

"Do you have any idea how long this will take to fix?" Sam asked quickly. She could estimate it, but his far greater experience with the Atlantis computers would make the estimate much more accurate.

"Excuse me?" He stared at her for a second, opening his mouth to speak then stopping to swallow. "I don't know. As I said earlier, I need more time to determine the extent of the damage. That'll take at least another eight to twelve hours. We're disconnecting all Earth based computers except for those in Gate operations. There are hundreds of them, and they have to be scanned and cleaned of any viruses. We need to isolate the functions so that we can work on the programming and keep them from getting re-infected."

"Can you ballpark it?" Ellis asked with an even tone.

Rodney was already worked up, so any question from that particular colonel was not well taken. He didn't even try to keep the annoyance out of his voice. "Well, it depends on how much of the programming I will need to go around and clean up after the…"

John repeated the question a little more forcibly. "Rodney. How long?"

The astrophysicist turned to snap but saw his friend exhale wearily. He quickly factored in time spent without access. "It could be a week, maybe more."

"A week?" Teyla was appalled at the notion, as they all were. "So long?"

"You have to remember that we won't have 24 hour access."

Ellis rubbed the back of his neck. "That's a long time to be defenseless."

McKay bristled even more at the perceived slight. "This is unbelievably complex programming that's been corrupted by…"

"We know, Rodney." Sam said gently as she held up a hand to stop him. "We have at least one advantage, though. No-one knows this location."

"And Sheppard can fire the drones from the chair." Ronon spoke for the first time.

Sheppard rubbed the back of his neck. "Maybe."

"Are you considering evacuating non-essential personnel?" Ellis asked.

The leader of Atlantis shook her head. "Not yet. We have no indication that we are in immediate danger and the Wraith don't know our whereabouts. I hope we can get this resolved before we have to consider evacuation."

The question left unanswered for all of them was how an evacuation might be accomplished. The Stargate was seemingly out of the question, leaving only the Apollo. They all knew she wasn't capable of transporting the entire population at once.

"Well, the Apollo will remain here as long as necessary." Ellis said then his eyes narrowed. "What I want to know is, who did it and when?"

"It must've been the Trust. Who else would have the manpower to put something like this together and the ability to get someone to Atlantis to plant it? They have the entire operating system. Remember when Caldwell was taken over by a Goa'uld?" McKay stopped only long enough to breathe in. "Oh my God, there could be a Goa'uld here again!"

Col. Carter wanted to move the meeting on. They were all tired and there was far too much work ahead of them. "Everyone coming from Earth, either through the Gate or on the Apollo or Daedalus, is screened. All personnel at the SGC are checked as well. There are no Goa'uld here."

"I read the report about the incident." Ellis said. "The Trust is the most likely source, but could it have been that Wraith you had here?"

"No. The computers he had access to were isolated from the city, and I checked them out myself after he left." McKay answered then went on a little smugly. "The Trojan is too complex and would have taken a team of experts familiar with the all of the city's programming months of work to pull this off. It had to be the Trust. They probably started working on this when Atlantis didn't blow up last year."

Most of the table quickly glanced at Sheppard then away again. His part in that incident was still too close to the surface.

"He's right." Sam tried to move on. "If not, we have an enemy on Earth we don't know about yet."

There was a momentary silence around the table as everyone absorbed that frightening idea.

Teyla suddenly asked, "Rodney, did you not say that you need the system active to work on the coding?"

"Yes, that's right."

"I was thinking about that." Sam had been watching Sheppard, but couldn't tell if he was listening. He was sitting next to McKay and he was staring at the astrophysicist's laptop screen. It was easy to see he was tired, more so than the rest of them. "John?"

It took him a moment, but John finally realized his name had been said. "Sorry."

"We need to find you some relief."

McKay's head snapped around. "Don't look at me. I'm going to be a little busy fixing this mess."

"I'll be fine." Sheppard already knew it was unlikely that anyone else would be able activate the system.

"We have a lot of people up here working on the coding. You can't sit there 24 hours a day until this is over." Sam reminded him. There were varying degrees of effort needed to use and control the technology but she hoped someone could be found to relieve him. She glanced through the open doors and saw it was now a little brighter. They had all been up for more than a full day and needed to get some rest. Mistakes now could push an already dangerous situation beyond retrieval.

"You can't expect me to do both." McKay grumbled, feeling like he was being asked to do too much.

"Rodney, you and Maj. Lorne probably have as much chance of being able to relieve Col. Sheppard as anyone." Zelenka pointed out.

"If you have any luck, we'll round up some others that have shown they can use the Ancient technology with some ease and have them try it." Sam insisted. If these two couldn't do it, no one else would be able to.

"Yes, Ma'am." Lorne agreed, but he wasn't too hopeful. His own attempts to activate individual functions hadn't worked so far.

With an audible and annoyed sigh, McKay nodded. "Fine. Maybe I can take my laptop with me and work while I'm sitting there."

"The Apollo can beam you over to save time." Ellis offered. He knew the chair room was in another tower and it would be a waste of time and effort to get there on foot.

"Thank you, Colonel. We appreciate it." Sam smiled and nodded. "If you don't mind, let's see how McKay and the major do in the chair first."

"Sure." Ellis said as he stood up and activated his radio.

Sheppard remained seated as everyone else began to move. "Do we know if the Jumpers have been affected? We need to see if we can get them out of the bay."

"Excuse me?" Ellis asked.

"We should move at least a couple of the Jumpers out if we can. We may need them later." He didn't feel the need to elaborate.

Rodney snapped his fingers. "Of course. He's right. The Jumpers are vital if, well, something should go wrong."

"Okay, we'll do that now, too. We need to verify they're clean of viruses first." Sam agreed.

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The light from the Apollo's beam faded, leaving Sheppard, McKay, Lorne and Ronon standing near the weapons chair. The emergency lights were supplemented by a portable light brought in earlier by the Marines.

"We're here." McKay said into his mic as he waved Lorne to the chair. "Go ahead."

Lorne glanced at Sheppard, who cocked his head toward the chair in agreement. Evan compressed his lips and exhaled heavily. He crossed to the chair and sat down then hesitantly placed his hands on the pads. For a moment, they thought the chair would activate, but it only glowed weakly then darkened again.

"Come on. Concentrate." McKay urged, still annoyed at being there. More than a slight fear he might not succeed nagged at his ego.

"Rodney." Sheppard admonished him.

Lorne took a deep breath and closed his eyes, pushing back as if trying to coax the chair to move. It repeated the momentary glow but that was all. He tried one more time with the same results.

"Okay, enough already." Rodney snapped as he strode with false confidence to the chair. Lorne jumped up to let him sit down. "Like I said, I can't sit here and work on the code at the same time."

He placed his hands on the pads and leaned back. Rather, he tried to lean back. Nothing happened. He scowled at the pads then shifted as if to get more comfortable. With a deep breath, Rodney carefully lowered his hands on the ATA pads again. He got the same results.

"Col. Sheppard, how's it going?" Sam asked through their radios.

He tapped his transceiver to speak. "Maj. Lorne didn't have much luck. Rodney's trying now."

"Shhh!" Rodney squirmed then tightly screwed his eyes closed in an effort to concentrate harder.

John caught Ronon rolling his eyes and, with a shake of the head, warned him not to goad the astrophysicist. He waited a little longer as Rodney tried in vain to activate the chair. Finally, after watching his frustration grow with the futile efforts, John decided to stop him.

"McKay."

"Just…let me concentrate. I can do this." He didn't want to admit defeat, and tried to push into the chair even more.

Sheppard approached him and spoke quietly. "Rodney. Stop. Like you said, you can't be here and working on the programming at the same time. So it doesn't matter."

The argument worked and gave McKay an out. He groaned loudly and opened his eyes as stood up. "I'm glad someone realizes my efforts are more useful somewhere else. Can we go back now?"

"Not yet. We need to get the Jumpers out of the bay." Sheppard sat in the chair. "Col. Carter, are the pilots ready?"

"Yes, they are, and the Jumpers have powered up normally."

"Stand by." He placed his hands on the pads and leaned back.

McKay was both relieved and dismayed at the seeming ease Sheppard had with it. He mumbled under his breath, "That's so not fair."

"The Jumpers seem to be unaffected by the viruses, John." Sam informed him a couple of minutes later. "They're clear of the tower. The Apollo is going to beam you back up here. Ready?"

Sheppard sat forward then stood up. He barely glanced at the others. "We're ready."

They gathered in Col. Carter's office this time. She was already sitting at her desk when they materialized. The meeting would be very short. Her gaze moved from McKay to Lorne then to Sheppard. "Any luck?"

"No, but I wasn't given much of an opportunity." McKay blurted out, making a point of looking at no-one. The thought of not being able to activate the chair was aggravating.

"No, Ma'am." Lorne shook his head, glancing at Sheppard with concern. He pursed his lips in thought, something Sam caught.

"What is it, Evan?"

"There was something, only for a moment, but it's weird." He frowned deeply. "Normally, there's kind of a feedback when you use the Ancient technology."

"What do you mean?" She asked.

"Well, there's always something that tells you it's working." He searched for an example. "Like when firing a drone, I know where it is and what it's doing. More or less. It's hard to describe. The sensation is even stronger when flying a Jumper."

McKay snapped his fingers. "Yes, yes. He's right."

"What?" Ronon asked.

McKay held up his hands, momentarily at a loss for words. "The best way to describe it is it's like the Ancient technology that needs the gene is almost like a living machine. It's kind of like AI, artificial intelligence."

"Like the Replicators?" Lorne asked.

"No. Yes. Sort of, I suppose. You can feel it responding, know what it's doing. Now there's nothing. It's dead." He spun around to stare at Sheppard. "How the hell are you doing it?"

"Doing what?" Sam asked, trying to follow. She'd heard only vague descriptions about how people with the gene used it. She knew it was often a matter of simply turning equipment on or off, but interactive use was also needed from time to time. No-one had ever given her a satisfactory explanation on the latter. Even Gen. O'Neill avoided the question.

"Turning everything on, that's what." McKay cast an exasperated glance at her before looking at Sheppard again. "The city is dead. The virus is effectively preventing us from initializing the systems. How are you doing it?"

John wearily sat on one of the chairs in front of the desk. He thought for a moment before shrugging. "I don't know."

Rodney wasn't accepting the answer. "You don't know?"

"No, Rodney, I don't." Sheppard folded his arms. He didn't even want to try to explain it. The intensity in his voice stopped McKay's response before it started. "At least it works. Okay?"

"Yes, it works." Sam stood up, understanding he didn't need this discussion right now. "Right. I think we all need to get some sleep."

"No. No. No. We can't stop now." Rodney shook his head. "There's too much to do."

"Rodney. We can't afford to make any mistakes." She said. This was going to take a lot of time and they needed to pace themselves. "It's 0712. Get something to eat and as much sleep as you can. We'll start again at 1300."

When McKay hesitated, she stood firm. "I mean it. You can't do anything without Col. Sheppard, and he is going to obey a direct order, aren't you?"

"Absolutely." John started for the door. This was one order he was happy to obey.

"Fine." Rodney muttered petulantly. He watched the others leave, trying to decide whether he should at least attempt further argument. Realizing she was right in that Sheppard was necessary, he began to follow them.

"Rodney. Wait a minute." Sam said as he got to the door.

"Yes?" He turned back, surprised she'd changed her mind. When he saw her gaze was on John's back, he asked, "What…?"

"I want everyone to get some rest, particularly John." She walked around her desk and perched on the edge of it.

"Oh? You think Sheppard's more important than anyone else?"

"Rodney."

"Well, just because he can…"

"How difficult is it for John to activate the Ancient technology right now?" She asked pointedly, keeping her voice low to avoid any possibility of being overheard. If everything hinged on Sheppard's ability to give them access to the system, she needed to know what kind of effort he was putting into it.

He glanced at the door, beginning to understand her concern. "I honestly don't know how he's doing it at all. There's nothing there. It's as near to dead as it can be without unplugging the ZPM and naquadah generators."

"There isn't any way to work on the system without him in the chair, is there?"

He shook his head slowly. "No. The viruses are incredibly complex and have invaded just about every vital function and sub-routine. We wouldn't even be able to get to it."

"What about writing a worm?"

Rodney shrugged. "I was thinking about that. It may be possible, but I need to see more. Whoever did this knows his business. There're all kinds of safeguards against tampering written into the virus and there are probably multiple copies hiding everywhere."

"That's what I thought." Sam said with resignation, already knowing the answer to the next question but wanting confirmation. "How long do you think this will take?"

"Five days, if we're very lucky if we work twenty hours a day and throw everyone that's remotely competent at it. There's no way in the world Sheppard can keep…" He stopped, feeling miserable.

She released a long breath and stood up. "Well, the Apollo is here for as long as we need her. We'll just have to do the best we can. Okay?"

"Yeah." He turned to leave.

"Get some sleep." She reminded him.

"Not much else I can do." He replied, shoulders slumping as he walked out of her office.