Chapter 3

Thirty minutes later when Sheppard arrived with Ronon. The handgun strapped to his leg was out of place over his civilian clothes. They stopped on the Gate room floor just long enough to check the security set up before climbing the stairs to the ops deck. Both were out of breath and sweating from running halfway across the city then up the nearly seventy flights of stairs.

"What the hell's going on?" John got out between gulps of air. He looked from Sam to Rodney then back again.

McKay jumped in immediately. "The Ancient technology is offline."

"We're not sure." Sam added.

McKay threw her a glance. "We can't initialize any of the Ancient systems." He paused. "Well, I could for about three seconds, but as soon as I took my hand off the ATA pad, it went dead. Now, nothing."

"John…" Sam started, but he was already walking around a console with one of the activation pads.

Sheppard rubbed his right hand on his hip and took a deep breath. The concern on his face eased only slightly as the console came to life as soon as his hand touched the pad. The large screen behind him glowed and data began to scroll down its length. It became lifeless again as soon as he backed away.

"Well, that's a lot of help." McKay muttered and turned back to the laptop. "Do it again."

Sam nodded and watched her laptop. Sheppard repeated the move, this time leaving his hand on the pad as McKay worked as fast as he could. He finally waved Sheppard away. Again, the console died.

"What happened?" John asked as he moved so that he could look over their shoulders at the screens.

"I don't know. It looks like it's the operating system. The problem is that we just can't get into it while it's offline." Sam replied slowly, thinking she was beginning to understand.

"Look, much of the Ancient technology needs someone with the gene to initialize it. Once initialized, all but a few functions run until turned off." McKay explained.

"I know, Rodney."

"Well, right now it isn't staying initialized, it's turning off as soon as we end contact with the ATA pad, and we can't get any of them to perform any functions." McKay reached out to the console with an ATA pad nearby and put his hand on it. This time nothing happened. "Half a dozen of us have tried to get anything to do more than light up, without luck. As far as we know, you're the only one that's been able to get it to actually work."

Sheppard frowned at him, not quite sure were he was going. "So? How does that help?"

McKay exhaled heavily, expressing his impatience. "We need the system running to find out what's wrong."

"John, we don't know what the problem is." Sam decided to take over the explanation. "We need to look through the program code to determine what's gone wrong and restore it. You seem to be the only person that can activate the system."

He started to walk back to the console. "Okay."

"No, no. That's not going to be enough. These controls just aren't going to give us the access to what we need." McKay stood up, looking around at the dead consoles. He suddenly snapped his fingers several times and pointed at Sheppard. "The chair. You can initialize the entire system and keep it active from the weapons chair."

"How long will it take?" Sheppard asked, suspecting an answer he wouldn't like.

"I don't know!" McKay snapped. "We have to figure out what's wrong first."

"Can't you just do the same thing you did on the Daedalus when the Wraith virus took over? Wouldn't it be easier to wipe the system and load a back-up?"

The astrophysicist closed his eyes and shook his head in frustration. "No, the systems here are far too complex and we don't know what the problem is yet."

Sheppard compressed his lips in thought then pointed towards the Gate room floor. "What about the pedestal Helia used?"

McKay shrugged. "We tried it, but couldn't get it to rise. You may have more luck."

Sheppard sprinted down the stairs but hesitated for a split second before trying to raise it, remembering what he had done the last time he used it. The near destruction of the city at his hands haunted him. He swallowed as he held his right hand parallel to the floor. A long moment passed before the small control pedestal appeared. He laid his hand on the pad and looked up at ops level.

"Anything?" The colonel asked loudly.

"Stand by." McKay's voice shouted back. Several minutes later he answered. "It isn't enough."

"Damn it." Sheppard muttered under his breath as the pedestal disappeared into the floor. He climbed the stairs two at a time.

Sam looked up from her laptop and shook her head. "It wasn't stable enough to really do anything. I think we have to see if the chair will give us better access to the system."

"Okay. Give me a few minutes to get down there." He turned and headed back down the stairs.

Ronon watched him disappear then looked at Col. Carter. She nodded and said, "Do you mind?"

"No." He hurried to catch up.

When Ronon fell in beside him, Sheppard said, "You don't need to come. It's just going to be boring."

"Nothing better to do." The Satedan half shrugged and kept walking.

As they reached the corridor leading to the route back down the tower, a group of technicians carrying portable lights, a naquada generator and other equipment passed on the way to the Gate room. It was now lit by the early afternoon sun, but would soon be in shadows. Similar equipment was being set up in the infirmary and the mess hall. They were grateful the late spring weather was warm enough to be comfortable day and night.

Sheppard's mind was racing as he and Ronon ran down the stairs. He'd felt nothing in the Ancient systems. The familiar sensation of knowing how the technology was reacting to his touch was absent. It was like Earth technology. Flip the switch to turn it on, cold and lifeless. Right now, the only way he knew it activated was because he could see it.

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Sam turned to Chuck. "See if you can get a signal to the Apollo. We need to get her back here."

"Yes, Ma'am."

A few minutes later, Chuck spoke quietly. "It's Col. Ellis, Ma'am."

She nodded and touched her transceiver. "Col. Ellis, this is Carter."

"What can we do for you, Colonel?"

"How fast can you get back here?"

"About ten hours. What's wrong?"

"All Ancient technology in the city is offline and we don't know why."

"We're on our way." He said without hesitation, knowing she wouldn't ask unless absolutely necessary. There was a pause. "Do you have the Gate, sensors, anything?"

Sam glanced at Rodney, who frowned and shook his head. "Nothing right now. We're blind."

"Sitting ducks." Rodney groaned miserably.

"We've barely been able to activate individual controls, and haven't been able to get any functioning." She glanced at her watch, wondering how long they would be vulnerable. "Can you check your sensors for us?"

"As we speak." Ellis responded. There was a pause. "Nothing in your vicinity."

"Thank you, Colonel. One more thing." She glanced at McKay. "Would you contact Midway for us? Let them know our situation and that we don't think they should try to dial in until we know more."

"Do you think it might be dangerous?"

"Probably not, but I want to be sure."

"Understood. Will do."

"Thank you, Colonel. See you in a few hours."

"We'll get there as soon as possible." Ellis signed off.

At least they knew the Apollo was on her way. She might not be able to protect them from a concerted attack, but she could be their eyes and ears.

McKay impatiently tapped his transceiver. He was impatient. "Sheppard are you there yet?"

"Not yet, Rodney." Sheppard snapped back. "Remember, the transporters aren't working."

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Two Marines were prying open the door as Sheppard and Ronon ran up the stairs near the chair room. Their flashlights helped the small amount of emergency lighting in the corridor. The pair slowed, gasping for breath as they walked into the room. Even though the trip from the Gate room was downstairs, they'd descended quickly then ran full speed from the central tower to the one housing this room. Sheppard looked around as he as he approached the chair. He was so accustomed to the city responding instantly to his presence that the darkness and silence were disturbing.

"We're here. Let's see if this works." He said as he sat down and placed his hands on the ATA pads. He breathed a sigh of relief and closed his eyes when the chair activated. It reclined but remained motionless. Lights in the room came on. "What do you need, Rodney?"

"We need access to the operating system." There was a pause. McKay was almost apologetic when he spoke again. "Uh, all of it. We don't know where the problem is, if it's systemic or isolated in key areas. Sorry."

"Great." Sheppard muttered to himself and inhaled deeply. He tried to relax as he exhaled. He was able to fly and land the city with the handicap of a single ZPM. Even if Atlantis felt lifeless, how hard was it going to be to keep the lights on for a while? He whispered, "Everything. Alright."

The city came to life. After that, it was impossible for Sheppard to know with certainty anything was happening. He felt nothing. The action was going on high up in the central tower, where who knew how many people were frantically searching the operating system for a bug, or bugs, big enough to bring the city to a standstill. He relied on their conversation coming through his transceiver to tell him it was working.

Ronon motioned for the Marines to continue their patrol. They quietly left as he moved a chair so that he could see anyone approaching the door as well as keep an eye on his friend. He had a feeling Sheppard was right. This was going to be boring.

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"I'm in!" McKay said with satisfaction. He glanced at Sam, who just nodded as she focused on her computer screen.

"Me, too." Zelenka and several other scientists and technicians chorused. Each was assigned a specific area of the system to search while they waited for Sheppard to reach the chair room. McKay and Carter would concentrate on those parts of the programming that governed activating and keeping the city's main operating system running. Zelenka had the Stargate programming. Everyone else had…well, everything else.

"Okay, you all know your assignments. Look, don't touch. If you find anything, just let me know." McKay used his most forceful tone. It was loud and clear that anyone who tried to dabble in repairs on their own would have their head handed to them on a platter.

The next few hours passed with growing frustration and doubt. It was immediately clear that someone had more than tampered with the programming.

"Rodney." Sam swallowed as she looked at him.

He was pale when he looked back at her. "We're screwed."

"Can someone tell me what's going on?" Sheppard's voice on their transceivers reminded them he was still in the chair. "What's wrong?"

"Sabotage, that's what's wrong." McKay replied. "The city's operating system has been attacked by a Trojan Horse. There's code in here overriding the Ancient programming. Layers of it. This is going to take days, weeks to figure out."

"Okay. So, what does that mean?" Sheppard asked slowly. His tone indicated he already knew the answer.

"John, this is Carter. At least for now, we can't keep the system functioning without your help." She saw the time. He'd been keeping the lights, and everything else on, for more than four hours without a word. She mentally kicked herself for being so engrossed that she forgot him. "Oh, God, I'm sorry. We'll stop for a while."

"What?" McKay gaped at her. "We need to get working on this now."

"Rodney, I could use a few minutes."

"But, you've just been sitting there." McKay blurted before he could stop himself.

"Not really."

"John, can you give us some time to give everyone a heads up." Sam asked, deliberately watching code scroll across the screen in front of her.

"Yeah." They could hear relief in his voice.

"I'll let you know when we're ready. Thank you." She turned to the tech at the communications console. "Give me city wide, please."

The young woman toggled a control and nodded.

"Can I have your attention, please? This is Col. Carter. We need to shut down the Ancient systems ASAP. Department heads, let me know when you're ready."

She knew everyone in the city had been scrambling to prepare for another shut down. Plans for the possibility that the city might one day lose power were already in place. Emergency supplies were stored in strategic locations. Four hours was a luxurious amount of time, so nearly all preparations were completed already. Right now, they needed to be sure no-one would be in danger of injury when the lights went out again. The first of them checked in immediately. The last department gave the all clear at the six minute mark.

"Okay, John. We're ready."

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"Thanks." Sheppard was aching to move. He lifted his hands from the pads and opened his eyes. Four plus hours sitting in the Ancient chair left him stiffer than he would have thought possible. Could be the fact the damn chair was made from metal and some other weird, rock hard materials. He vaguely wondered if they did it on purpose to prevent anyone dozing off.

Ronon, listening to the brief exchange, grabbed the flashlights and stood up. Sitting around was not one of his strong points. He knew it wasn't one of Sheppard's either. He frowned when Sheppard merely leaned forward but didn't get up.

"You okay?"

"Yeah." John nodded then stood up. He grimaced as he stretched cramped muscles then adjusted the transceiver in his ear. "Col. Carter?"

"Yes, John."

"I'll be back in a few minutes."

"Take an hour. We need to compare notes, anyway. Just let us know when you're ready to start again."

"Will do." John said then turned the vox off on his radio and rolled his shoulders as he walked to the door. "Come on, let's get something to eat."

Ronon's stomach growled in agreement. "I was wondering when you'd get hungry."

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Col. Carter pushed back from the console and looked around at the personnel sitting at various consoles and finally settled on McKay. "What do you think?"

Everyone followed her gaze to the chief scientist, not daring speak up first. He didn't take long.

"We are screwed." He said it quietly, much more so than anyone expected.

"McKay." Sam said flatly.

He waved at the computer. "Beside the master operating system, it looks like every function vital to running and protecting Atlantis has a virus specifically written to attack that it. I found at least a dozen and there're probably more. We have to isolate and work on them individually."

"Where did it, they, come from?" Sam frowned at her laptop then at him. "When could they have been loaded onto the system?"

"It had to be recently. There was no evidence of viruses the last time a full sweep was done." He stopped and snapped his fingers several times. "We need to disconnect all Earth based computers from the city's system and scan them for viruses one by one."

"Yes, yes." Zelenka agreed. "There may be copies hidden on any one, or more, of them."

Sam nodded. "Okay, you two get your departments started on it. I'll make a city wide announcement, but we also need to set up search teams. Whoever planted the virus may have hidden a computer somewhere."

"It could be anywhere in the city." Zelenka frowned at the thought of searching the entire city.

"True, but we have to start somewhere."

"It's probably someone who went back to Earth last week. It'd be too much of a risk of being discovered to have a laptop sitting out there for too long." McKay pointed out.

"We can target the quarters and work areas of anyone who returned to Earth, but we'll start with anyone who went back in the last month." Sam looked at the two scientists. "Where would you hide a computer if you had to?"

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Sheppard stood in front of the weapons chair, scratching the stubble on his chin. He wasn't looking forward to sitting in it again, even for a few minutes. The impression he had earlier in the control room was more than reinforced in the first thirty minutes in the chair. The city was as close to dead as she could get without being destroyed. She couldn't talk to him and her silence made it extremely difficult. The dull ache that had been behind his eyes for days was worsening. Well, he thought to himself, at least the other shoe finally dropped.

He could feel Ronon watching him as he sat down, but the dim emergency lighting hid the Satedan's expression. "Look, you don't need to stick around."

"I've got nothing better to do." Ronon took up position in the chair again.

"Okay." It was no use arguing, so he turned his transceiver to vox. "Col. Carter, are you ready?"

"Yes, John. We're ready."

He shifted in a futile effort to make himself comfortable on the hard surface before placing his hands on the pads. A moment later, the city was alive again, at least to everyone else. It was going to be a long night.