AN: I'm sorry for the long delay. I had originally envisioned this "episode" as being two chapters (the first of which would have been posted earlier) but when I got to the point I was going to split it at I realized it would be slightly cruel to leave you with the cliff hanger I envisioned if I didn't have the second part ready to go up relatively soon. So I just kept writing and, well, ended just making it one big chapter. Hopefully it was worth the wait.

Disclaimer: I do not own Chuck or Alias.

Chuck versus The Change of Base

September 8, 2008

Chuck ducked slightly keeping out of sight as much as possible. Slinking around the corner, he pressed his back to the wall, hoping that his pursuer would pass him by without stopping. Finally, as he maneuvered his way around one last corner he saw his exit. He would have to be out in the open for a few feet. Glancing around, carefully, he waited until there was an adequate distraction then made a run for it. Once he was three or four rows deep into the parking lot he finally slowed down and breathed a sigh of relief. Big Mike had been unusually vigilant about his employee's breaks since back-to-school shopping season had started with the first of September. As well intentioned as Big Mike might be, there was no way Chuck was going to let him interrupt his lunch time ritual. Especially since, for the last week, it had been more or less the only time he had gotten to see Sarah.

After their return from the Alps, construction on Castle had finally started. Unfortunately that meant that Sarah had had to stay at Castle and supervise the construction every night this week.

Chuck wound his way through the parking lot, glancing back every few moments to make sure that Lester or Jeff hadn't tattled to Big Mike about his little excursion, before eventually making it to the Orange Orange without incident.

As he walked through the doors to the shop a tiny bell rung announcing his arrival. Chuck wasn't sure if the bell had been added for extra authenticity or as a primitive early warning system. Probably a bit of both. At the sound, Sarah looked up at him with a slightly weary smile. He walked over towards the register, and he leaned over, meeting her lips with his over the counter.

"I missed you last night." He told her after they pulled away. Sarah grimaced slightly.

"It was so late by the time they packed up for the night it didn't seem worth it to drive back home when I'd only to have to turn right around and come right back to open the store." She told him. Hearing the frustration in her voice he realized that as much as he might want to complain about the situation, he needed to be the optimistic one right now.

"At least when this is done we'll have a nice shiny new base." He reminded her, then added with a slight smile. "With some nice lockable closets." She answered with a coy smile of her own, and they leaned in again for another short kiss. Then another.

"That will be nice." She breathed, between kisses. She sounded exhausted. Leaning back slightly he realized that she had shadows underneath her eyes.

"Did you get any sleep last night?" He asked, slightly concerned.

"An hour or so in the back room." Chuck frowned slightly and she added, "Alex is coming in this afternoon. I'm going to go back to the apartment and get a few hours sleep before I have to come back tonight." Alex was slowly packing up for her big move later this month. Chuck doubted she would be able to relieve Sarah for very long, or that Sarah would let her. The fact that she had asked Alex to come in at all probably was indicative of just how little sleep Sarah had been getting since the Construction had begun. Truthfully, he hadn't exactly been sleeping very well himself without her there.

"Maybe I can have an onsite install this afternoon." He said. She just chuckled.

"I think that would sort of defeat the purpose of returning the apartment to rest." She pointed out with a smile, then leaned in again for yet another kiss. This time he rested his hands along her neck, pulling her in for a deeper kiss. At some point he thought he heard the tiny bell on the door ring again, but was too wrapped up in his girlfriend's lips to really think about. Eventually they were interrupted by the sound of someone behind him very purposefully clearing her throat. Chuck glanced over and realized with some embarrassment that it was an actual customer. He pulled away and gave the woman a slightly bashful smile before turning back towards Sarah.

"I guess I'll just have my usual." He said. Sarah flashed her own bashful smile towards both him and the customer, before turning to swirl out the yogurt. "Could you make one for Casey too." He added as she began scooping on his toppings. "He's wound pretty tight right now." Sarah gave him a knowing smile. Casey might be enjoy his time between missions more in this timeline, but that didn't mean that a week with no sign of any gun play didn't begin to grate on him. Sarah finally handed him the two yogurts, and he snuck a final peck on the lips before heading out. He tried to ignore the glare from the woman that had interrupted them as he navigated out of the store balancing a yogurt in each hand.

He found Casey, unsurprisingly, in the large appliance section. Casey growled slightly as Chuck handed him the yogurt, a sound Chuck chose to interpret as the Casey equivalent to thank you. Once Chuck had gotten back to the Nerd Herd desk he glanced over towards large appliances again and smiled slightly with amusement when he saw Casey tucking into the yogurt.

Chuck had been dealing with customers for just over an hour when his phone rang. Looking down there was simply a text.

"Get to the airstrip ASAP. Will brief in flight." Chuck glanced over towards Casey who nodded toward the door and the Orange Orange and Chuck headed out to grab Sarah.

XXX

"Earlier today a fire alarm was triggered automatically from inside of Leeryder Industries main facility. The alarm was patched directly into the nearest fire department. When they arrived, they discovered the building had gone into a total lockdown. Nothing could get in or out. In order to help determine what they were dealing with, they eventually conducted an aerial infrared scan. There was no fire. More disturbingly, there were no heat signatures to suggest any of the employees were inside, despite the fact that none of the employees' families have been able to contact them. Not even those of the two founders of Leeryder." Beckman told them once they were in the air.

"As bizarre as this seems General, what is our stake in this?" Casey asked.

"Leeryder finances its research by selling cutting edge weaponry to the highest bidder. We have no idea what may have triggered the building lockdown, but it may well be a biological weapon, radiation or other toxins. Even without considering the technology Leeryder may have on site, we can't risk someone attempting to steal the weapon information inside and letting the contaminate out." Graham ground out.

"You will be meeting a local hazmat team. They will be setting up a portal decontamination unit outside your entry point and you will be given containment suits. We need to determine what happened and bring any dangerous materials or weapons to a secure location."

"What about the local authorities? Or the European agencies? Aren't they going to want to deal with this?" Chuck interjected.

"One of Leeryder's founders and many of their employees are American. And for some reason, the other agencies don't seem to have a problem with us sending our agents into the building first." Beckman said, with a sarcastic quirk of her lip. "If the area proves not to be contaminated, or you find something particularly interesting, that may change. That means, this may be your only chance to examine what's inside the building. So be quick, be careful and be thorough." With that cheerful thought, both of their bosses left them alone to plan.

September 9, 2008 (Local Time)

The suits were designed to block radiation, disease and whatever else could be inside. They were also cumbersome and heavy. A small little boy part of him couldn't help but geek out at the fact they bared a certain resemblance to space-suits. Then that little part of him realized that he was about to enter a building filled with an unknown contaminate that most likely killed all the people inside and it ran away and hid under its metaphorical covers.

They used a laser to burn through the doors, making sure to keep the opening contained with the make-shift decontamination area. Part of the lockdown procedure was to stop any experiments currently running, and inside was eerily quiet. Aside from a few scattered papers and overturned dishes, everything seemed in place, as if the workers were coming back at any moment. But there were no people, and no bodies. The only thing out of place were the small piles of ash that were scattered through the rooms, and the occasional scorch mark. Otherwise the building looked like it was in the middle of a fire drill.

The plan was to head to the main computer room and hopefully find a record of what had caused the lockdown. Along the way they were to take samples of the air and anything else that was suspicious. Something about the ash piles tickled at the back of Chuck's mind but he couldn't remember why. He still suggested they take separate samples from a few to test.

Once they reached the server room he was infinitely glad that they had thought to modify his suit to give him extra dexterity. He might be good with computers, but even he would have trouble hacking into the system by hunting and pecking in oven mitts.

Once he had gotten in to the system he found himself staring at the screen, dumbfounded.

"What is it Bartowski? I know this is nerd nirvana but our air packs give us a limited timeline." Casey groused. Chuck shook off his shock and attempted a couple of other ideas before he had finally run out of ways he knew to explore the servers.

"There's nothing here." He said, still befuddled. "All of the data's been chomped on by a virus. K. K. virus. Sort of. All that's left is bits and pieces and the virus itself. "

"You mean that kid we saved back in July did this?" Casey said, anger rising in his voice.

"No, no. It's been modified. It would take me a while to figure out exactly how, but Beckman gave me a copy of K.K.'s code after our run in with the Ring on our last mission. They wanted to make sure it really was a failsafe, and the Ring wasn't trying to throw us off." He told him.

"How long will it take?" Sarah asked carefully.

"Too long." Chuck told her simply. "I'll download it and look at it later. According to the maps here, there's another server room on one of the upper floors that didn't show up in our schematics. Maybe that one wasn't infected." He suggested.

While he downloaded what was left of the servers onto a specially designed drive, Casey and Sarah looked around a bit more. They still only came up with more of the same. Nothing out of place, and no people. It was the same as they walked towards the second server room.

At first Chuck thought it too had been infected by the virus. But once he poked around a bit he realized, to his shock, that was not the case. There was no virus. All of the multi-teraflop machine, all of that space and computing power of this second bank of servers had been designed only to run one program. It was designed to run only that one program.

"Anything?" Sarah asked.

"The room wasn't a back-up for the one downstairs. It's all to run a piece of equipment in the next room, from what I can tell." He told her, still not sure what could require so much computing power to run. Then, a thought occurred to him, and he, slightly warily, walked over and opened the door to the room beyond.

He went in only a few feet, and stood there, frozen and staring. Casey and Sarah walked in behind, staring as well, as if they were trying to figure out what was before them, or simply why it fascinated him.

On the left of the room was a server. It wasn't large, only a fraction of what Castle would have. If this machine was what he thought it was, then the operators must be routinely manually transferring anything stored on it to the room downstairs. There was no way it would be able to hold everything it would need to otherwise.

On the other side of the room was a chair that looked eerily like the one that had been used on him in Thailand, complete with wires ending in electrodes hanging limply over one of the arms.

In the center was a contraption that would best be described as looking like some unnatural mating of a coat rack, one of those outdoor heaters they have at restaurants and a mechanical tree. It was attached by a thick rope of cable to both the chair, the server and the room behind them.

It wasn't like the machine that had brought him back. That would be like saying that ENIAC was like the Roark 7, or perhaps more accurately that ENIAC was the same as a cutting edge computer produced in fifty or even a hundred years. But there was enough of the backbone of this contraption in that machine that his engineering eye could see that it was its ancestor.

"So, all that's for a chair?" Casey asked disbelievingly.

"I don't know." He told Casey. "I guess." Telling the lie to Casey made guilt weld up in his gut, but they had a limited time they could stay inside the building in their suits, and none of it was delegated to explaining why he had a fair idea what the chair was for.

He still couldn't help but stare in shock at the device that, only this morning had been purely a hypothetical contraption to him. His father had been right. Leeryder had found a way to control the intrusions, or at least channel them. And they weren't simply storing them on a server; they must be downloading information into people. It wasn't like the Intersect, which at its base was a computer program, but a direct download from one person to another. From one time or timeline to another.

He had to swallow down a bit of gorge as he imagined what that must feel like. Years ago when he had been subjected to the much more advanced machine he had felt like he had the worst hangover of his life for three or four days afterwards. This machine was far cruder.

Chuck moved over towards the server on the far side. He suspected that this was where they downloaded programs and schematics, but at the moment it was empty. He turned around to face Sarah and Casey again, shaking his head.

"Whatever this is I have a feeling we don't want someone else to get a hold of it." Chuck said, his eyes unconsciously drifting towards the chair. Both his partners followed his gaze slightly. Sarah gave an enthusiastic node. Casey grunted.

They split up. Casey and Sara began to pull off pieces more or less at random, from the device as none of them were really sure what might or might not make the contraption no longer viable. Chuck worked on the servers in the previous room. He was torn as to whether or not he should destroy the program completely, or try to download it. The computer and science fiction geek in him wanted so badly to see what they had come up with. But he knew better. As long as this existed, there was a chance it would get into the wrong hands. And so he started working to destroy it.

Since he was in the outer room, he was the one to hear the voices first.

"We have company." He whispered over the com. Chuck realized that he no longer had time for the subtle approach, and he began pulling out the servers and trying to rip out the most important pieces as Sarah and Casey moved into the room.

They pulled the door open and began sneaking through corridors until they caught sight of a small group of men dressed in containment suits. Chuck only got a glimpse of enough of one of them to flash. The man's file suggested he worked for Adelbert de Smet. Chuck supposed that made sense. Leeryder's lab was reasonably close to The Belgian's European headquarters and he was just the sort of man to have both buy weapons from Leeryder, and have no qualms about scavenging off them now. The men turned slightly and saw them.

Chuck forced a flash, but there wasn't exactly a program in the Intersect that fit. Fighting in a containment suit was a bit like fighting the Stay Puff Marshmallow man while dressed as the Michelin Tire Man. If both were terrified of deflating with the slightest touch or jostle since, depending on what exactly had happened here, any breach of their containment suits could be just a fatale as a gunshot.

After a few minutes of being gentle, however, Chuck realized that they'd be stuck here forever if they continued their cautious dance and simply kicked the man that had zeroed in on him in the gut. When his opponent intuitively curled down, he gave him a calculated hit along the neck that knocked him unconscious. With his man down Chuck turned to find he wasn't the only one who had decided to stop being careful. One of the guards had grabbed a letter opener from a desk and threw it towards Sarah.

Instinctively he dove forward, tackling Sarah out of way. He then heard a large crash and looked up, to see that Casey had chucked something at the man that had thrown the dagger like office accessory that was large enough to knock him unconscious. Pushing himself up, Chuck offered Sarah his hand. When she took it a burning pain erupted from his shoulder and his fingers unconsciously weakened. Sarah looked up in concern and he saw her eyes widen. Following her gaze he looked over his own shoulder and saw the letter opener that he had tried to block was sticking out of it.

He stared at it numbly, his brain automatically cataloguing the injury. Ordinarily he would have been lucky. The knife-like object had missed any bones or major arteries. He wouldn't even need that much physical therapy to heal the muscles. But that was only if he lived long enough to worry about it. While the lack of bodies had made Chuck fairly sure they weren't dealing with a biological weapon, he wouldn't have staked his life on that instinct. Now, his suit was breached and he didn't have any other hope.

Casey took out the last remaining man, then turned toward them.

"Get him out of here." He told Sarah. Sarah stared at Casey a moment before his words sunk in. She grabbed Chuck's other arms and pulled, but Chuck held his ground.

"That machine Casey, we can't let anyone get to it." He said, no longer trying to temper the urgency in his voice. If he was going to be dead soon anyway, there was no use in hiding how much he feared what that machine could do.

"I'll take care of it, just go." Casey growled. Chuck finally allowed Sarah go guide him towards the exit.

XXX

Sarah held onto Chuck's hand through the thick dish washing glove- like protrusion into his room so tight that she was fairly sure she was cutting off his circulation. The thing was designed to give doctors access to a patient in one of the infectious disease containment rooms without having to put on a containment suit, but as soon as the doctors had finished fussing over Chuck she had claimed one as her own.

After she had finally gotten Chuck to leave the building, he had been placed into his own personal containment bubble. Once they were sure he was stable the bio-hazard team had happily sent him, along with all of their samples to Washington and out of their country. The airplane the CIA had secured them even seemed to sense the urgency she felt and somehow traversed the Atlantic even faster than the normal CIA jets. The doctors had done more tests than she had known existed on Chuck then retreated, leaving her and Chuck alone to wait for the results of both to his own tests and to the tests on the various samples they had taken.

As a rational Agent Sarah knew that this was all precautionary. If there had been a biological weapon or some other substance released in the building that had killed those inside, there would have been bodies. If it had been something so virulent that it had destroyed the bodies before their arrival and it had still been in the air, Chuck wouldn't still be alive.

The worried Girlfriend Sarah, however, couldn't help but be terrified. Sitting in the hospital, she and Chuck found themselves in the oddly reversed position of having him try to comfort her from within his hospital room while she held onto to his hand as if she could literally keep him with her with her grip. He had pulled up a chair to the glass wall so she could hold his hand, and their heads had almost unconsciously leaned together against the glass.

Casey had arrived a few hours after they had. He had moved out of Chuck's eye line and begun to pace not long afterwards. Finally, the doors to the ward opened allowing three men inside. The taller one in the middle wore a lab coat and was obviously a doctor. She was so focused on him, she hardly noticed the other two.

"I'm just here to let you know that we got the results from both the tests done on Agent Bartowski and on the various samples you collected. We didn't find anything unusual. So." Sarah suddenly felt like she could breathe again.

The doctor held up a key card with a flourish and swiped it along the door, unlocking Chuck's room. Chuck ran out and immediately grabbed her, sweeping her up and turning her around into a deep kiss that continued once her feet had hit the ground. She vaguely heard the doctor excuse himself in the background and a chorus of uncomfortable throat clearing from the two remaining men as she sunk into Chuck's lips and finally allowed herself to relax. Then Casey grunted.

"Your gown Bartowski." He ground out. Chuck stiffened and pulled back a little, looking behind himself. He blushed slightly then ran back into his room, coming out a moment later wrapped in a blanket, and still a bit pink. It was then that she noticed exactly who else had come to speak to them. Both men were shorter and slighter than Chuck and Casey, but that really wasn't saying much compared to the general population. One she recognized as Kris Kinkaid, the other appeared familiar but she couldn't place his name.

"I'm Manoosh, by the way." The previously unknown man said holding out his hand. She smiled as she reached out to finally shake the hand to Chuck's friend.

"It's nice to finally meet you." She told him. Chuck exchanged nods with Manoosh and Kincaid before he readjusted his blanket so that he could reach out his arm to take her hand again.

"So, what are you two doing here." He asked, settling in beside her.

"Beckman and Graham asked K.K. to help me look over the virus you found." Manoosh explained. "You were right, by the way. Twice actually." He added. "It was a modified version of K.K.'s virus on Leeryder's main server."

"More like butchered." K.K. grumbled. Casey let out a grunt which Sarah translated as something along the lines of how could you be so concerned about your stupid code when people are missing.

Chuck attempted to defuse the situation slightly by putting his hand up between the two men and seemingly trying to hold Casey back by sheer power of will. And perhaps Casey's fear that in trying to separate them Chuck's blanket would fall off.

"Why don't you explain how the virus was modified?" Chuck encouraged. "Maybe that will give us an idea of what happened."

"Well, my virus, it was designed to be stealthy. Like a software ninja." Kincaid said, becoming slightly enthused as he talked about his creation. "It was supposed to sneak in unnoticed, copy and transfer all the files on a server than erase itself, so no one would know it had been there. But whoever used my virus on that server chopped up the sequence that was designed to start the deletion sequence. Instead it triggered, clumsily I might add, a bit of code that sent a message to one of the lab. We think it turned one of the pieces of equipment there."

"Which lab?" Chuck interrupted, urgently.

"H 15, I think. It was on the third floor." Sarah could see Chuck relax slightly at the realization that it hadn't been the lab with the device they had found that had been activated. While Chuck had yet to directly tell her so, given all that had happened since they had found the odd contraption, Chuck's reaction when he saw the device had all but confirmed to her that he believed it was how Leeryder had been tapping into other timelines.

"The schematics we've found seem to indicate it was used for some sort of testing of micro pulses on Organic matter." Manoosh added. Chuck's brow furrowed a moment before smoothing out again.

"Was there anything else added?" He asked Kincaid.

"Well, after the signal was sent, the modified code started the lock down procedure, and then triggered the deletion sequence. But they twisted it so instead of doing what it was intended for, it would delete everything other than the virus." Kincaid concluded. Chuck stared off a moment before turning back to Manoosh.

"You said I was right twice?" Chuck asked..

"Right. About the ash. You were right to have it tested. There wasn't much left, but we were able to tell what it was." Manoosh hesitated a moment. "Well, it was human remains." Manoosh finally said, looking slightly sick.

"Human remains? What could have done that with lighting up the whole building?" Casey asked. Manoosh only shrugged. Suddenly Chuck's eyes grew wide.

"Firebomb." Chuck yelled out. Both she and Casey looked at him questioningly. He took a breath, then and began to hurriedly speak. "The lab testing micro pulses on organic matter. All living things incinerated but nothing else." Chuck said, as if that was an explanation. Suddenly both Manoosh and Kincaid's eyes went wide.

"Firebomb." They chorused, slightly excited as they caught on to what Chuck was suggesting. Then they quickly seemed to sober.

"And for those of us that don't speak geek?" Casey asked. Manoosh glanced at Casey and her, apparently trying to size up how much he would need to paraphrase.

"There was an episode on, well, on a TV show called Firebomb. In it the bad guys used a Neutron Bomb that sent out micro pulses. It disintegrated organic matter, but left everything else unharmed and it managed to do so without leaving any kind of lingering radiation. So all that was left afterwards was ashes and skeletal remains. " Manoosh answered. "But that kind of technology can't exist, right?" He said, almost pleading.

Sarah looked towards Chuck, and their eyes met momentarily for a knowing glance. It might not exist in their universe, but how to create such a device must have existed in another.

"Apparently." Chuck said, soberly. Both Kincaid and Manoosh appeared to shiver slightly at the thought.

"We can't let something like that sit around." Casey stated.

"You should probable move quickly. Once the European agencies find out that the buildings have been cleared," Manoosh began to point out.

"They won't be so keen on having us be the ones inside." Chuck finished. "Have you guys briefed Beckman or Graham?" He asked, turning back towards his friend and Kincaid. The two shook their heads. "I still need to be officially released. Casey, why don't you go with them to let Graham and Beckman know what's going on? Then Sarah and I can meet you at the airfield. And I can get pants."

Casey grunted in agreement and went with the two other nerds. Sarah suspected it had mostly to do with Casey's desire to have Chuck be fully clothed as soon as possible, rather than an acknowledgement of her boyfriend's ability to plan.

XXX

Their second breach of the former headquarters of Leeryder Industries was far more like their usual missions, complete with mission gear, sneaking in, skirting around security and the possibility of being caught by an agent of a foreign government. While the General had officially delayed sending the test results to the local authorities, that didn't mean they hadn't already learned of them, so She, Chuck and Casey decided not to chance being turned away at the entrance.

This time they already knew what they were looking for and where it was, approximately, even if they had no idea what it looked like. Given how Chuck had described the similar device on Television, Sarah doubted it would look similar. As it turned out, it was relatively easily to find. The lab all seemed to entirely center around one box-like metal contraption. They placed the device into a specially constructed container Manoosh had slapped together before they left. Hopefully, it would keep the device from activating, and provide some insulation from its affects if it was accidentally triggered. Theoretically at least. Then they had slipped back out a back entrance.

Despite the relative easiness of the mission, however, Sarah noticed that Chuck still looked weary and worried on the flight home. She knew that partly had to do with the ordeal with his suit and his time in the hospital. She hadn't been the only one scared and the kind of tiredness that follows running on adrenaline for as long as they had wasn't something wiped out by the few hours of sleep they had gotten on the plane over. He also still had a knife wound in his shoulder. Technically he shouldn't have even been allowed back into the field so soon, but it had been a three man job and with so many possible players involved neither Beckman or Graham had trusted another team to do it.

There was more too, through. While they had waited for Chuck to be officially released from the Hospital, he had confirmed her suspicions about the device they had found in the second computer lab. He believed it was Leeryder's way of tapping into other timelines and possibly an antecedent to the device that had sent him back in the first place. Pulling up the armrest between them, she scooted over so that Chuck could wrap his arm around her shoulder.

"What are you worrying about now?" She asked him, resting her head in the crook of his arm. She felt as Chuck let out a sigh then glanced towards where Casey was snoring, to make sure their partner was really asleep.

"If it was K.K.'s virus that was used on Leeryder's database, that means that the Ring now has everything that was on their main server." Chuck told her. "We barely were able to beat them before, who knows what they have access to now."

"Do you think they can replicate the device?" She asked. It was a terrifying thought. An Organization such as the Ring having access to the kinds of weapons and technologies that Leeryder may have collected in their database was scary enough. Having them have access to an unlimited number of possible weapons from an unknown number of timelines and dimensions was something that would be almost unthinkable.

"I don't think so. That system was isolated from everything else and there was no sign that K.K.'s virus was on those servers. But if they did…" He didn't need to finish the thought. She pulled herself closer to him. In any other circumstances the position would have been comforting, cozy even. But despite being tired and cuddled up against each other, neither one of them were able to fall asleep on the way home.