A/N: Just a little one shot I thought of while reading another fic. I wish I could tell you which but I can't locate it and there are WAY too many fanfics called "Chuck Vs. The Intersect" or something similiar.

Sarah walked numbly into the courtyard where Chuck Bartowski, her asset, and the one she secretly loved lived with his sister. She wasn't quite sure what she was doing there, just that she was. She knew she had to do something but she wasn't quite sure what or where to start. A new thing for her.

She was Sarah Walker, CIA spy extraordinaire. But right now she felt numb, confused and lost and not quite sure what was really going on. And wishing she had spent more time listening to Chuck and Morgan whenever they babbled about their sci-fi stuff.

"Walker, let's go, briefing in five." Casey grunted coming up behind her and turning to go to his apartment next to Chucks.

She remembered then. Yes, protocol dictated a debrief with the General. So she entered the apartment slowly behind Casey and watched him as he flittered around the room getting things ready. He retrieved a bottle of water from the fridge and walked it over to her, strangely kind and handed it to her.

"Drink this." He said simply. She took the bottle from him, her fingers numb and barely touching it. Walking further into the living room the screen blinked black for a second erasing the NSA symbol that idly swirled bringing up General Beckman sitting behind her desk. Sarah sat heavily on the couch in front of the screen.

"What is the status?" Beckman barked out at the two sitting there. She had not been pleased to get a message from Casey stating that the Intersect, both of them have been compromised.

Casey looked at Sarah for a moment to see if she would be the one to report. When she didn't' say anything other than stare off frozen into space he stood at his full height to report in.

"General, the Intersect has been taken. Apparently for an indeterminate amount of time." He stated. Beckman looked at him stunned.

"What exactly do you mean by that Major?" She said coldly. Casey wasn't exactly sure himself as he wasn't there. He gently prodded Sarah who still hadn't spoken up.

"Walker." He hissed at her. Still nothing. Beckman put on her most stern and annoyed looked she could possibly have, losing patience with these two.

"Agent Walker, I demand you report immediately what happened at the warehouse tonight. It was a simple recon mission to determine what had happened to communications in the building. How could it have gone wrong?" She demanded. Still nothing from Sarah. She looked back at Casey. "Major?"

"General the surveillance equipment that Bartowski and Walker were equipped with only worked until they were in the elevator. After that everything was cut off. From what I saw of the first floor before they entered there was no one around. Aside from that everything looked normal." He reported.

"It wasn't." Sarah said softly. They both looked at her.

"What was that Agent Walker?" Beckman said. Sarah finally looked up at the screen.

"It wasn't normal. Nothing was. Everything was wrong but I didn't see it." Beckman and Casey shared a look.

"What wasn't normal? Why didn't you get out of there once communications were down?" Beckman said. But Sarah had said all she would, her mind going numb again.

She had to find a way to help Chuck. There was no way she was going to leave him there in that building with that thing. Whatever it was. It wasn't him, she knew that now but now she knew and now she could fight it.

She blinked out of her numb haze, looking around the room. Her eyes widened at all the electronic devices around. Cameras and security, everything. Her eyes suddenly fell on Beckman, horror filling her senses. He was watching them. She knew he was. How could he not, he's the intersect.

She stood up quickly from her spot ignoring the protests of Casey and General Beckman. She ran over to the closet behind the front door where she knew Casey kept the device jammer, the strongest the NSA could create. She just hopped it was strong enough to fool the Intersect. Grabbing it she quickly came back out and stood in front of the screen.

"General, it's watching us." She said simply as she pressed the button to activate the jammer. Immediately the screen went black as connection was lost and alarms sounded through the room as all electronic surveillance devices went offline.

"What the hell are you doing Walker?" Casey said grabbing the jammer. He looked at the horror on her face and softened his look a bit. "What is going on Sarah? What has you so spooked? What happened to Bartowski?" She was silent a few moments before shaking her head, then looking him in the eyes.

"I honestly don't know, but whatever it is, we have to save him."

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"Six Months Previous."

"The Intersect computer is up and running. It's already started spitting out results and creating leads for us to follow. It appears to be working the way it was planned to in the first place." General Diane Beckman stated into screen, looking amongst her team, dubbed "Team Bartowski."

She watched as they sat rigidly in their seats around the conference table in Castle waiting for her report on the progress of the new Intersect that was to be turned on and made operational after the last four weeks of testing. Beckman was kind of taken aback by the team's lack of enthusiasm, being as they would be the most effected with it.

"You will be given the results of the readouts for perusal before they are to go out to other teams to follow up on." She paused, still nothing from them. "Furthermore you will continue to check over the results the Intersect throws out until such a time as we are confident that the results are genuine."

Beckman paused again, waiting for confirmation. She put on her stern face and looked directly at them.

"Is there a problem folks?" She finally asked. The others looked around at each other, not sure what/if anything should be said. Finally Sarah Walker sat up straighter to begin to speak.

"It's nothing really General, we were just concerned that with the new Intersect up and based on the results if…" She couldn't even finish the sentence. She looked over at Casey and then Chuck.

Beckman understood what they were asking. It has been something that had been discussed at length with the higher ups. The termination of the human Intersect once the machine was brought online. She had spent an enormous amount of time to prep for that meeting, citing the merits of keeping Chuck Bartowski around. She would never admit it to them but she had grown fond of him too over the past two years.

"You're worried that a termination order will be given once the Intersect is fully operational and its results verified." She stated for them. Nobody answered just stared straight ahead into the screen. "Rest assured that there will be no such order. It has been determined that even with the new Intersect, having Chuck on as an analyst as well as a portable version would be a great advantage in the field." She stated.

"Well, glad to know how important the Intersect is to the government but what about me?" Chuck asked warily. He was actually getting tired of being treated and talked about like a machine, with them ignoring the fact that he is a human and has a life he would like to get back to.

"I don't understand Mr. Bartowski. I thought you would be pleased to know you would not be terminated." Beckman asked confused. Chuck quirked his eyebrow wondering if she was intentionally being clueless or if she was secretly this way in real life.

"I mean, don't' get me wrong General, I'm happy, stoked, elated, whatever adjective works best for you that it's been decided not to just off me when I'm not really useful but you see, I'm just not sure if this is what I want to do for like, ever. " General Beckman stared at him unblinkingly, making Chuck feel more nervous.

"I mean you guys have been great you know, getting my degree back, even though technically it was because you were trying to get me that I lost it in the first place, and you know the constant terror and life threatening situations and-"

"Mr. Bartowski what exactly are you talking about." Beckman finally broke his tirade off annoyed.

"I'm just saying General, that, I'm no spy. I'm just a regular guy. I'm not made for this." He said simply. Beckman stared at him for a few minutes, unnerving him further before sighing deeply, softening her eyes as she spoke directly to him.

"Mr. Bartowski…Chuck. I fully understand your situation. You never signed up for this, and I understand that it is not exactly what you wanted in your life. But unfortunately it did and this is the way it has to be. With you in this position and in the field it makes you useful and as much of a liability. The Joint Chiefs believe it is the best solution to keep you around." She stated leaning forward. The realization hit Chuck hard and he felt a wave of defeat wash over him.

"So you're saying Chuck's only permitted to live at the discretion of the government based off how useful he is?" Sarah asked her angry showing through.

"Yes Agent Walker that is exactly what I'm saying. It will be more prudent to have the two of you there watching him if he was useful as an agent instead of just running around LA."

"But General I'm not an Agent. I'm a normal guy stuck in an extraordinary situation." Chuck protested weakly. The General looked over a moment before responding.

"That's exactly right Mr. Bartowski. The Agency has decided it's time for you to stop being just and asset and to become a spy. Agents Casey and Walker are in charge of training you with the additional help of others when needed and available." She announced.

Casey and Sarah looked at each other eyes wide. They were not expecting that. Casey then looked annoyed at having to spend extra time with Chuck trying to teach him how to stay alive. Sarah on the other hand was terrified of what it meant.

Chuck was a kind sweet man who could barely stand to literally kill a fly. She knew that being a spy changes you, and not for the better. She already saw changes in Chuck between now and when she first met him. He was less innocent, less shocked. He already spent time out of the car on missions much to her dismay instead of being afraid and staying. She was worried how being a full time Agent would change him forever.

"General, I'm not spy. I never was one, and I never can be. I just…I don't have what it takes to be one. I'm just an ordinary guy, with special skills aside from fixing computers." He said dejected. Beckman was starting to lose her patience with this.

"Regardless of what you feel Mr. Bartowski we have all seen how you are on missions. You may not be, and never will be the most traditional of spies but whatever you do you have made this team one of the most successful the CIA and NSA have ever seen. The higher ups are eager to see what you can do with a bit of training. I empathize you wish to get back to your life but this is the only solution there is for you. You will be a spy, like it or not, good luck." With that she abruptly ended the transmission.

Nobody talked or moved for the next several minutes, each lost in their own thoughts on what happened. This whole situation seemed to be getting out of control for Chuck. He had been delighted a few weeks ago when General Beckman informed them of the new Intersect being almost ready to start. He thought he was finally going to move on, hopefully with one Sarah Walker. However Casey quickly burst that bubble he was in as he mentioned quickly and quietly to Sarah once the General cut out that she had better start putting together a getaway plan for her and Chuck.

That lead to one of the most awkward conversations he's ever had with the big bad NSA Agent. And that's saying something considering how Casey was. Finding out that he was literally a breath away from being terminated all those months ago, and it was someone who he considered a friend who was going to do it really hit Chuck in a way he never felt before. He'd been betrayed over and over again by those he trusted, starting with his own parents. He thought hearing that Casey was going to kill him due to orders wouldn't affect him as bad as it had but he was wrong.

An awkward heart to heart with Casey a week later helped relieve some of his apprehension, thought he never believe he would fully be able to trust him again. Casey admitted that he struggled with that order and if push comes to shove he didn't really think he would have been able to pull it off. Casey blew it off as a moot point to think about now anyways since the appearance of Sarah at the door informing Chuck of the last intersects destruction had caused him to pull away anyways. Whether Casey would have gone through with the order would be an answer they would never get.

"Well that was a cheery briefing." Chuck said to the blank screen. He stood up from his spot and immediately headed for the stairs.

"Chuck, where are you going?" Sarah asked concerned. Knowing chuck he was brimming to the top with emotions that he would need/want to get out, so he surprised her by just leaving. Chuck stopped at the top of the stairs annoyed, leaning over the banner down at her.

"Where do you think I'm going? I'm going back to the Buy More to finish my shift. It's where I'm going to end up for the rest of my life so I might as well not get fired from it. "With that he turned and excited the lair into the elevator.

Sarah sighed and returned to the conference Area where Casey still sat staring into space. She sat down in her chair across from him and stared till he looked back at her.

"What do you think of this?" She asked simply. Casey thought deeply for a moment before answering.

"Honestly I don't know Walker. This Intersect computer sounds like it could be a major asset to the intelligence community. Look at Bartowski, he's only half what this computer can do and we do a good job." He stated, avoiding what he knew Sarah wanted to know.

"You know very well that's not what I mean Casey. I meant about Chuck becoming a spy. "She said annoyed.

"I know that's what you mean and honestly I think it's a good thing." Sarah sat up straighter, confused at that.

"What do you mean a good thing? It will change him. He won't be the same Chuck." She protested.

"And that's a bad thing?" Casey grunted out, as Sarah glared hard at him. Finally he relented. He hated talking about feelings especially if they involved Chuck Bartowski. "Look, the kid is extremely smart and resourceful. He's done and exceeded everything I never thought he could possibly do. Honestly Walker with a bit of training, Chuck Bartowski could become one of the best spies ever."

Sarah was shocked by his honesty and thought deeply on his words. He was right about Chuck. Despite training or anything he had been amazing with all the spy stuff, and became even more so as he gained confidence. He barely screamed and ran away anymore, which scared and relieved her at the same.

"But there are some aspects to being a spy that I don't think he's ever really grasped. There are some parts I don't think he could handle, and if he was made to do could destroy him." She said honestly worried. Casey considered this for a moment.

"Then it's a good thing he has us then isn't it?" With that he stood up from the table and followed the same path as Chuck out the door and back to the Buy More."

"I certainly hope he does." She said softly to herself.

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'Present'

Sarah hadn't explained further on what exactly had happened at the warehouse with Chuck and Casey was starting to get annoyed. Since she cut off all communications outside the apartment all she did was run back and forth across his apartment putting together a small arsenal. He figured he should stop her but as she seemed to be quiet and planning something he decided to wait.

A loud pounding on his door caused him to startle for a second. He started heading for it when Sarah blocked him and pulled out a gun.

"Walker-"He started to protest but she gave him a glare and he shut up and rolled his eyes. She crept to the door and peaked out the peep hole seeing Ellie standing there.

"Who is it?" Sarah asked. Ellie stopped looking around for a moment and looked at the door.

"Sarah? Is that you? Is John around? I have a call for him." She said through the door.

"Tell me what you did your first night in med school." Sarah shouted back. If Casey was confused before he was doubly confused now.

"What? Sarah, what is…?"

"Just tell me Ellie." She pressed. Ellie took a deep breath.

"Alright, I spent two hours on the phone with Chuck and then met up with Devon who I had just had random sex in a supply close with. That's how we met." She said exasperated.

Casey looked impressed at that. He always thought Ellie, while the older wiser one was the wilder of the two.

Sarah opened the door to let her in, looking behind Ellie to make sure nobody had followed her. Ellie looked really confused as she walked over to Casey.

"I have a woman on the phone who called me when she couldn't get ahold of you. She said it's extremely important that you contact her back." With that she handed the phone to Casey who brought it to his ear to find it dead. 'Of course, the jammer is still on.' He thought to himself.

"Seems she got disconnected, I'll just step out and call her back." With that he took his phone and walked out of the building. Ellie took that moment to look at Sarah, eyes widening at seeing her hold a gun. She stepped back a bit bumping into a table, looking down at it behind her seeing more weapons.

"Oh my god. What is going on?" She asked. "Where's Chuck" she practically shouted stepping closer to Sarah. Sarah still hadn't responded just stared at Ellie. "SARAH!" Ellie shouted at "Where is my brother."

Finally Sarah broke; she fell to the floor tears falling down her face. Ellie immediate went to her and kneeled down. Casey walked in at that moment seeing the two women on the floor.

"He's gone. He's gone, I don't know how or why but he is and we need to save him." She sobbed out. Ellie looked up at Casey confused but was not comforted to see his own confused expression.

"What do you mean he's gone Sarah? Where did he go? Is he alright?" She asked shaking her gently to get her attention.

Sounds began filling the room as the electronic surveillance equipment hummed to life. Ellie startled looking around as the screens came on. She stood up looking at the main monitor seeing the living room and chucks room of her apartment. Confused she stared at them for a moment before turning to Casey.

"What…What is all this? Are you spying on us John? Are you some kind of perv?" she demanded angrily.

But then the screen went blank for a moment before the screen popped up with an image of them in the room. Ellie and Casey looked around for which camera it was before finding it in the corner. Sarah had stood up then, face went and eyes red from crying and came back to stand next to them.

"It broke through the jammer. It's watching us." She said simply, staring at herself on the large TV Screen. Casey turned the TV screen off breaking off everyone's concentration on it.

"That was General Beckman. She is on her way here to brief in person. I suggest you get your story straight Walker." He said gruffly before turning towards the kitchen. "Would you like some tea Bartowski?" He shouted back to Ellie. But she didn't hear him she was concentrating on Sarah.

"What's watching us Sarah? And for the last time, where is Chuck. I have to know." She said calmly, or as calm as she could. She always got worked up whenever it came to Chuck.

"Someplace horrible." Sarah whispered.

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'Five months previous'

The Intersect computer had been exceeding all expectations. Spies all over the world were gathering further intel and criminals were being captured at a record breaking rate. Technicians worked around the clock keeping the computer up to date and running, making sure everything ran smoothly.

One slight issue that arouse however was how through the computer had become. It had been created in order to learn better algorithms and build within itself better search engines for the best results possible. Anytime someone put in a negative or positive into the computer it would learn through that and make it stronger. It was essentially teaching and building itself.

The computer had access to any and all data bases in the world and frequently scanned each technician or entrant into the building, spitting out results of potential thought not likely threats. The Intersect had found one of the technicians to be associated with an arms dealer by referencing him through millions of people twenty or more times removed. It had been determined after that that a team would be needed to filter out results before handing them out to teams.

While crews were working on some diagnostics one day in the clean room, where the main console was held, the crews were talking about some exploit one of the spy teams had recently been involved in. The computer frequently scanning any and all names, dates, places, anything said in the building scanned for one Agent Carmichael.

Once the search came up with a classified file, classified at a level as the computer in question it began digging further as it had the highest clearance possible, as well as creating its own code to break down any potential online security. The term "Intersect" came up in the search and the computer dug further, learning everything it could about it.

The Intersect computer learned of Agent Charles Carmichaels' real name; Chuck Irving Bartowski. Learned how he was practically and orphan, raised by a sister, very intelligent getting into Stanford on a full scholarship. It learned of an Agent Bryce Larkin's betrayal getting him expelled to which he now worked at a Buy More.

Accessing his files the Intersect watched thousands of hours of video, read email, everything and anything available on this human before finally coming to its own realization.

'This human was a part of it. He was part of the Intersect.'

With that thought the computer went back through watching all the danger the human had been in over the years, the missions, the plots, or just driving the Nerd Herder vehicle to work. This human, like all humans were, was in frequent danger, was fragile, and could easily be harmed.

With that in mind the Intersect computer began to plan.

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'Present time'

Four hours after the General contacted Casey she arrived at a little private airport outside of Los Angeles. Once she stepped off the plane and onto the tarmac she was greeted with the solemn faces of both Agent Walker and Casey and to her surprise Dr. Ellie Bartowski.

"What is the meaning of this?" She demanded at seeing Ellie. Sarah kept her face firm. They had tried to convince Ellie to stay home and let them deal with this but once she found out the Chuck was missing and in trouble they couldn't. The best they could do was tranq her and she promised that when she woke up she would do everything she could to get in the way and find Chuck, so they reluctantly dragged her along.

Though secretly they both felt that she would be a great asset in attempting to retrieve Chuck, if not in the after when they got him. He may need immediate medical assistance and she would be a great help then.

"General, Ellie was there during the whole commotion in Casey's apartment once you called and everything came back on. She found out about the situation, and we feel she could be a huge help in this. "

The General listened but kept her stern expression on but accepted the answer. In truth she'd been debating bringing her in on the team as a medical expert to research and keep track on the intersect in Chuck.

"Very well, so tell me, what exactly is going on that you couldn't tell me over secure line." She inquired stepping closer to them. Casey signaled that they should walk farther away from the plane, signaling the Generals guards to remain.

"Alright walker, we're here in the middle of an empty field away from all electronic devices. Now would be a good time to finally tell us what is going on.

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'Two months ago"

Chuck Bartowski sat behind the Nerd Herd desk logging invoices from installs and such that the Nerd Herd provided. He didn't have so many to keep him busy but he logged everyone else's as well. It was policy to do it yourself but as the Nerd Herd supervisor and therefore responsible for any unlogged invoices he felt it was easier to just do it himself correctly the first time rather than have to go back and correct everyone else's work. He was aware that he was not helping his fellow employees learn better skills or responsibility in the work place, but he felt he had too much to do as it was to deal with it.

"Hey" A feminine voice jumped out in front of him startling him. He glanced up to see Sarah Walker leaning on the counter in her Orange Orange outfit. A smile jumped on face unable to prevent it.

"Hey you, how's business at the semi Asian frozen yogurt business." He said looking up from his logs. She leaned forward towards him and he did the same placing a small kiss on her lips before backing up. Sarah gave him an amused look at his insecurity of PDA's.

"Life is good there. You know, with no business and all. Makes coming over to see my boyfriend at the Buy More easier." She stated. Chuck nodded his agreement.

"Of course if you had more stable hours and didn't take off at all hours of the day people might be more inclined to buy yogurt." He said. Sarah agreed, but she knew she wouldn't do anything about it. She hated working that cover job.

"Please tell me we have a mission. I can't take this monotony today. My finger is starting to twitch and itch." Casey said coming up beside her in his green Buy More shirt. Chuck had to agree. Today had been an unusually slow day for them with hardly any customers in the store.

"Sorry Casey nothing yet. The eggheads are still going through results before giving missions to the General to issue."

"Hey! I take offense to the term 'eggheads'" Chuck protested. Sarah just smiled at him.

"In any case there is no mission, yet." Sarah finished. Casey growled at her response, they hadn't been on a mission in over three weeks.

"BARTOWSKI" Big Mike shouted from his office door. Everyone looked over at him. "You have an install, get to it." With that he slammed his door shut, most likely going back to his donuts.

Chuck sighed and began gathering his gear he would need and printing out the invoice from the system. Sarah looked annoyed at the way Big Mike just yelled at him from across the store like he was a dog, while Casey just grunted and returned to work.

"Where is this install?" Sarah asked curiously. She grabbed his hand and held it once he stepped out from behind the desk, walking him out the door. Chuck looked down at the invoice.

"It's in part of the old industrial area. It looks like a company is setting up there and they need a technician to help hook up the computer systems." He said blandly resisting the urge to sigh. It was going to be a long day, he could tell. Sarah's eyes scrunched together grabbing the paper from him and looking at the address, noting it wasn't too far from the secret location where the Intersect was being housed in an eight story building.

"Do you want me to tag along? I could go as an assistant or back up." She offered, hoping he would take her up on it. She knew the kind of criminals and other people who hung around in industrial areas. But he shook his head no.

"It'll be fine. I have all my panic buttons and GPS's on me for you to track me. It's just a simple install that has a lot of installing to do." He placated. Sarah stood on her toes and gave him a kiss on the lips again and wrapped her arms around his neck as she would to a real boyfriend.

"Just be careful ok?" She said into his ear. A shudder went down his spine as her breath hit his ear. He pulled away reluctantly.

"Always." He said simply and headed towards his Nerd Herder.

Forty minutes later, made longer due to traffic on the freeway Chuck arrived at his destination. It was an empty looking building from the outside and its abandoned appearance along with the building surrounding it with the same look sent shivers down his spine. He reasoned with himself that the owners kept it like this for a reason, perhaps to prevent them from being robbed while they set everything up.

He knocked on the door and waited for someone to answer. His head turned to the right as he heard the soft zip of a camera moving and he smiled and waved at the camera sitting in the corner there. He heard the loud bang behind the door as it unlocked itself and opened on its own accord. He figured that the owners meant for him to let himself in.

He walked inside having a hard time seeing. The whole room was bathed in darkness except for strips of light pouring in from cracks in windows.

"Hello?" He shouted in the darkness. His voice echoed all around him telling him the building was for the most part empty. He felt another chill as he turned to leave as quickly as possible but was stopped as the door quickly slammed shut and locked. He turned the handle and banged on the door a few times to try to get it open but it wouldn't budge.

Giving up he turned back around facing the room breathing quickly. He was about to press the panic alarm on his watch when he heard sounds of a video playing coming from a room near the back. Against better judgment he walked through the building, careful to not step on any unknown thing and into the room beyond.

The room had a bit more light then the one behind him. The windows clearly been cleared of the boards that covered them. In the room was a plain table with an old unstable looking computer chair in front of it and a computer. The room was slightly lite from whatever was on the screen indicating the computer was on, though Chuck couldn't image that the building actually had any power.

He stepped closer to the computer. The screen was white with black words blinking in the middle saying

'Hello Chuck'

Chuck looked around the room frantically, wondering who would set this up and what kind of trap it was. He looked back at the screen for a second and it flashed quickly showing a bunch of random images. Chuck's mind immediately soaked them up; gaining the intel that was on them.

His eyes glazed over as he stared further at the screen. It flashed again, more images, telling him to sit in the chair. He complied zombie like, not taking his eyes from the words 'Hello Chuck' still there as if nothing happened.

He blinked a few times, his mind telling him that something was wrong and he once again reached to press the alarm on his watch but was unable too. The screen blinked black and more images coming at a rapid pace. Chuck was helpless as his expression slackened and he watched the screen unable to turn away.

An Indeterminate amount of time later it stopped. And everything went black.

XX

Chuck Bartowski walked back into the Buy More three hours later. He strode in with confidence and an eager smile on his face. Looking around he noted that most everyone was gone for the day and looking at the watch on his left wrist noted it was quitting time for him as well.

He went behind the Nerd Herd desk, sitting down in the chair there in front of the computer screen deciding he should log the invoice before quitting.

Sarah saw him from the Orange Orange enter the store and was puzzled that he didn't stop by first to inform her he was fine. It wasn't exactly required but it was a courteously he always did knowing how much she tended to worry on the longer installations he was required to go on.

She quickly left the Orange Orange, putting up the "closed for the day' sign and making it over to the Buy More. She saw him sitting at the Nerd desk in front of the computer and walked up quickly to him.

"Hey, Chuck, how'd it go?" She asked as casually as possible. Chuck looked up her and his eyes went distant for a moment, but not in the same way as a flash would before he smiled brightly and stood up extending his hand.

"Sarah Walker, it's nice to see you. The install went great and the customers are happy." He said adding a huge smile to it. Sarah looked at him warily.

"Yes, it's me." She said simply. She leaned over the counter a bit to get a kiss. Chuck paused for a moment his eyes going distant again for a second before he leaned over and pressed a full on kiss on her lips. Sarah was shocked by it, expecting a small chaste kiss as always but she didn't let it go to waste.

He pulled away from her and she felt her heart beat faster as she reluctantly stepped back. He smiled a bright gleaming smile showing off his full white teeth.

"How about I finish this invoice and then we go get some dinner?" He suggested. Sarah thought for a moment before agreeing. It would be good for the cover.

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'Present Time'

Sarah took a deep breath trying to decide where to being. What she was about to say would make her sound crazy she knew but it was the truth and it needed to be said so they could come up with the best course of action.

"Two months ago Chuck went on an install to the industrial district. When he came back he seemed totally different. He was calmer, confident, nothing seemed to faze him. He would occasionally go blank for a moment but he wasn't flashing and then he would come back with whatever we were talking about."

"Well Sarah, honey, Chuck is very intelligent." Ellie said defending her brother. Sarah gave her a wary look.

"I know but this was different. This wasn't just Chuck with a lot of knowledge. This was as if he was reading a book to me." She turned to Casey then. "Haven't you noticed how much he improved so quickly in the training and on missions? He's flawless; everything he's done is flawless."

Casey thought for a moment going over the last couple months. Sarah was right. He seemed to be a new man. He fought hard, learned quickly and never made a mistake. He was stronger, faster, and more intelligent.

"Yeah, now I think about it he has. But Bartowski's always been a hard worker. What exactly are you implying Walker." He said. Sarah looked finally at General Beckman who seemed to be losing patience with them all.

"You gave us the order General, when communications to the Intersect was cut and we couldn't determine what happened or what was going on. You sent us to go in and assess the situation."

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'Twenty-four hours previous'

"Your mission team is to infiltrate the Intersect building and find out what is going on in there. All attempts at communication have not been successful. The last communication was three days ago when the technicians sent the current reports for missions. However we are unsure if they are the ones who sent them and for how long." General Beckman stated to the room.

Casey, Sarah, and Chuck stood in front of the screen getting their orders. They knew how serious the situation was and took the mission seriously. The screen split showing the eight story building.

"The first level is just office space and security. The next floor is empty and trapped with various security measures. Third level is research and development. The Intersect main console which is where you need to get to is on the fourth floor and you must enter from the bottom. The top floors from the roof is blocked up and rigged with security measures as well. Gaining entry from the roof is impossible."

The screen went back to Beckman full screen.

"We have entered you into the database in order to gain full access to the facility but we want you to be extremely cautious. There is no telling what is going on in there and what has happened. Do what you must to get in, gather the intel and get out. We will ask questions and forgiveness later. Any questions?" She stated.

The three in the room glanced at each other before finally shaking their heads no. They understood their orders. Find out what's going on and get out to report it.

"Good, in that case you leave in one hour. I suggest you get ready for the worst." With that the screen blinked out and went black before the NSA logo appeared.

"Well this'll be fun." Casey growled out turning around to enter the armory. Sarah followed close behind.

"So what's the plan? We all go or should one of us stay in the van?" Sarah asked him, obviously hinting at who should stay in the van. Casey thought about it for a moment, agreeing that it would be safer for Chuck monitoring instead of going in but Chuck was the Intersect.

"No, I'll stay in the van. We need someone to be able to relay the mission in case of an emergency. Bartowski being the Intersect may have an advantage and you're best to handle him so you two should go in. "Sarah was stunned.

"Wait, are you suggesting that you don't go in the building? Pass up a chance to blow things up and kill people?" She asked shocked. Casey rolled his eyes at her.

"What I'm suggesting is that there are billions of tax payers money pooled into that entire building and it would be best if as little damage to it as possible was made during this endeavor. Meaning you and Bartowski would be the best. "He said.

Sarah held in her laugh she wanted to make. John Casey was a full on patriot. His main hobbies and skills were blowing things up, killing people, and general chaos, but wasting money the good American people put out must trump that.

A few hours later Chuck and Sarah entered the front door. It was relatively easy to Sarah's surprise; they just walked in and entered their code. There was nobody on the bottom main office that they could see. The lights were on bright, the place looking like it had been occupied recently, however there were nobody around. The whole place seemed eerily vacant.

"Anything to report yet Walker?" Casey's voice rang over in her earpiece. She raised her watch to her wrist before speaking.

"Negative. The whole area seems to be abandoned. We're check out a bit more of the bottom floor before heading towards the elevator." He reported.

Sarah looked around each room and hall they entered. Everything seemed as she had told Casey, abandoned, however she felt the hairs on the back of her neck prickle up. She looked over at Chuck momentarily, seeing him not concerned. Chuck seemed focused on the task at hand, more focused than normal.

She had noticed over the past couple months how much Chuck had changed. Not only on missions and spy related areas but also in his personal life. He had stopped his babbling, stopped complaining about wanting a real life. He became very compliant and confident always do everything as ordered without complaint with a smile on his face. He had stopped for the most part playing his video games and reading his comics, the one time he did he beat whatever game it was in under an hour, a feat that impressed Morgan to this day.

Instead he spent a lot of time on the computer and in the Castle systems, going over data and manuals, learning everything he could. He made suggestions that were put into effect for better security and was really impressing the higher ups. In short, he was becoming the spy they always wanted him to be but at the same time she felt she was losing the Chuck she was falling in love with.

Even Ellie had noticed the difference, coming to her several times asking if everything was alright. With no further information and no indication that anything was wrong she could only tell Ellie that everything was fine.

Sarah felt the security cameras move to follow them as they walked down the hall to the elevator. She glanced up at each of them as she passed, looking them directly in the lens. She wondered who it was that was watching them so closely. She turned to ask Chuck but when he seemed unconcerned she didn't bother.

She entered the code and moved her eye to the retina scan to gain access to the elevator. A moment later the doors drew open allowing them to enter. She stood next to Chuck punching in the long stream of code that would allow them to bypass all other security measures and head straight to the fourth floor. She stared at the corner where the camera was unnerved by it.

"Chuck, who do you think is watching us?" She asked quietly, not taking her eyes off it. When Chuck didn't answer she finally turned to him. His eyes were glazed and staring straight as if his mind was elsewhere. "Chuck?" She said quietly.

When she got no response she grabbed his arm and shook it gently. He shook his head as if coming out of a trance and stared down at her with a hard expression in his eyes momentarily before they quickly returned to their normal state. A chill ran through Sarah as she stared back at him, feeling as if something was wrong.

"Casey, we should abort mission. Something strange is going on." Sarah said into her watch. She didn't get a response so she tried again. Her heart began racing turning into full Agent mode.

She turned from Chuck and began pressing buttons trying to stop the elevator, but it was no use, it slowly continued to make its way up, stopping frequently for its security scans. She was about to bust the buttons off when a tight grasp grabbed her arm. She looked up to see Chuck glaring down at her.

"I wouldn't do that if I were you Agent Walker." He said simply, not letting go of her arm. Sarah looked stunned for a moment trying to snatch her arm back. She finally succeeded as he let go of it and she fell backwards into the elevator wall hard. She massaged her arm noting that there would be a bruise forming soon.

"Chuck, what the hell." She shouted at him. But he ignored her and stood in front of the doors as the elevator finally stopped and opened up. He stepped to the side looking at her expectantly.

"Are you coming Agent Walker." He said. She noted the cold volume of his voice and shook her head.

"I think we need to be going Chuck. We need to get Casey." She said staying close to the wall. Chucks' face hardened further.

"That will not be necessary Agent Walker. Please come with me." With that he turned away from her and stepped out. She wasn't sure what to do. Everything in her being told her to get out of there but she couldn't leave Chuck there no matter how odd he was acting.

She pushed herself away from the wall and walked to the door. Her mouth fell open as she excited. There were consoles surrounding her in the large room and a glass window separating the room from the largest looking computer she had ever seen. The room that lay beyond was white and steel and practically glowing from the brightness of the lights.

"What…What is this?" She asked awed and still wary. Chuck stepped closer to the window and looked down.

"This is the Intersect. This is me." He said quietly. She glanced over at him confused.

"This isn't you Chuck. This is just a computer. You are you." She said without conviction. She felt her heart tighten at hearing him state he's a computer. It had always been a worry of hers that others treated him as a machine and not as a person; she never wanted him to actually feel like it.

Chuck turned to her then, his eyes distant once more. It was beginning to really unnerve her. A few moments later he came back out and looked directly at her.

"I have something to show you Agent Walker." He said simply.

"Sarah." She said back, looking determinately at him. He looked confused for a moment tilting his head slightly.

"Excuse me?" He said in way of confusion. But she didn't back down.

"It's Sarah. Why are you calling me Agent Walker Chuck?" She asked him taking a step closer. His next words frightened her.

"Because you are an Agent and I am the Intersect. Come." He said turning away from her stunned look. He walked to the side and pressed more codes opening the door leading down into the Intersect room. Sarah shielded her eyes from the brightness as they made their way across to a door on the opposite side.

Sarah looked around best she could for signs of anybody else, any of the technicians that were supposedly supposed to be here maintaining this computer.

"Where is everyone?" She said aloud, not really expecting an answer. Chuck stopped outside the large grey door and turned back to her.

"They have been found to be incapable of their duties and have been discharged." He said coolly. She looked at him trying to read him.

"And what does that mean? Where have they been taken?" Everything in her mind screamed at her to run but she was unable to. A part of her still screamed that this was Chuck.

"That is none of your concern Agent Walker. You have been found to be very competent and effective in your line of work and you have been chosen for a great task." He said.

"And what is that Chuck." She asked him. He stepped back and slid his palm on the panel next to the door, it scanned his hand and then the door opened.

The room beyond was bathed in darkness, a sharp contrast to the current room she was in. The only lights were up above causing dim light to shine around. She looked up at Chuck as he stared into the room unmoving, obviously waiting for her to make her move into the room. She stepped slowly in to it, letting her eyes adjust a moment before looking around.

There were machines all over and little robots controlling them. They moved back and forth around ignoring her presence as if she were just a blank wall. She was stunned, thinking back on all the reports she's read regarding the Intersect and not once reading about robots being part of the program.

She stepped further into the room, trying to avoid stepping on some of the tinier machines when her eyes reached the center. There on a platform in the middle of the room was a body of a tall man lying flat with machines surrounding him. She stepped closer seeing needles with fluids going to and from him. She gasped loudly as she finally approached close enough to see who the person was and she ran the rest of the way to the platform.

There lay Chuck, eyes closed, fluttering back and forth as if sleeping deeply. She raised her hand to brush it through his hair which was longer now and slightly dirty. He was pale with a sheen of sweat covering him. A blanket covered his body holy showing part of his naked chest as his arms lay on his side above the blanket. Her heart sped up as she quickly turned away from him to stare at the Chuck who still stood at the door.

"What is this? What is going on? Who are you?" She demanded coming closer to him with each step. He didn't flinch as she got right into his face.

"You Agent walker are tasked to guard the human. That is why you were brought here." He said simply. She was still shocked and now getting angry.

"Who are you?" She demanded once more. He looked down at her his eyes once again going distant for a moment.

"I am the Intersect in physical form." He said simply. "Modeled after the human Intersect."

"But why? Why did you take him?" She cried out in frustration.

Chuck or the thing parading as Chuck stepped into the room finally and walked over to the platform where the real Chuck laid. He looked down upon him with reverence in his eyes. Sarah walked up beside him, resisting the urge to rip his hand off for touching her Chuck.

"The simple answer Agent Walker is he is us. He is an Intersect. He is a part of us and he needed protection. Humans are so fragile. He could easily be hurt and terminated. It was decided that he must be protected at all cost and was brought here." He explained. She looked down at her Chuck, and ran light fingers over the side of his face.

"He dreams of you." The Intersect says next to her. It startles her to hear. She looked over at him momentarily but its focus is solely on Chuck. "He sleeps and he dreams. We can see it. They are beautiful dreams. It is why you were chosen." Finally he looked at her.

"Chosen for what exactly." She struggled out, the tears finally falling down her face.

"To protect him." He whispered to her. She was about to say something to him but was startled as alarms sounded loudly through the room. The Intersect next to her looked up and around as if they could see what was causing it.

"Stay here." He demanded as he marched quickly out of the room. She watched him turn around and shut and lock the door behind him, locking her in. She looked around the room seeing the robots still maintaining whatever tasks they were set to perform before looking down at Chuck again. She startled to see his eyes opened staring distantly to the ceiling.

"Chuck?" She whispered to him, coming close. She saw the monitor opposite her blink on with a black background for a moment before words appeared on it.

"Door in back. Follow Lupo, RUN!" it said simply. She reread it several times before looking down at Chuck again.

"Chuck?" She asked again, frightened. The screen turned blank again before more words appeared.

"No time. You must leave. Help me" It said. Tears fell faster from her eyes.

"I'm not going to leave you Chuck." She said simply. Once again the screen went blank.

"Come back for me. Leave." With that the screen blinked black once more and turned off. She looked down at Chuck to see his eyes had closed once more.

"Chuck!" She shouted to him trying to get him to open his eyes again. She was startled to feel a little tug at her pant leg. Looking down and screeching lightly she noticed a tiny little robot there trying to get her attention.

"Are you Lupo?" she asked it, suddenly feeling silly for talking to a robot. It did a little circle before heading to a wall opposite where she stood. She followed it as he tapped the wall indicating there was something behind it. She searched around before noticing a hidden latch at the top.

She flipped it and the wall turned slightly showing a staircase. Lupo the robot immediately went through and started going down the stairs by rotating its wheels and little robot arms. Sarah followed behind, startling as the door closed behind her. Reaching the bottom floor the robot indicated to be lifted to which she hesitantly did. It reached out to the panel next to the door pressing the keys with a poker finger allowing the door to open.

She held it for him but he stayed back pointing at her to leave before turning back to go up the stairs. She had to find Casey and get out. She had to rescue Chuck.

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'Present Time"

"Are you telling us Agent Walker that Chuck Bartowski has been some kind of robot for the past two or so months?" General Beckman said incredulously. Sarah's face started turning red, she knew how this sounded.

"That's not possible Sarah. There is no technology so far that can create a machine as realistic as what you're implying. It's still in the realm of science fiction." Ellie said. She put her hand on Sarah's back in comfort but Sarah pulled way.

"Look I know it sounds crazy but it's the truth. That machine is millions times smarter than us. It possesses the capabilities to process anything. Who's to say it hasn't figured out a way to create machines like this fake Chuck." She looked around the group desperately, hoping to see some kind of sign that they believed her. "Am I the only one who noticed Chuck behaving differently?"

"No. I've noticed it too. I just shucked it up to the kid finally taking things seriously, but you're right. He's been very un-Chuck like." Casey said. They all looked to Ellie next, who seemed to be deep in her own thoughts. Sarah gently nudged her and she looked up quickly noticing they were waiting for her to say something.

"Don't' look at me. He's been acting strange since last year when you guys showed up almost two years ago." She said annoyed.

General Beckman took a deep breath considering her options before her. She turned slightly to the guard by the plan and gave him some kind of signal. He disappeared on the planned for a moment and the General turned back to them.

"Well whatever the situation really is science fiction or not we have to gain control back of that facility and everything within it. We have over fifty people in there that are missing that we need to locate so I'm bringing one more person on your team." With that she turned back to the plan just as someone started exiting.

Bryce Larkin exited the plane, standing tall at the top of the stairs. Sarah heard Casey grunt in annoyance as he turned away to look in the opposite of direction. Sarah looked over at Ellie noticing her shocked expression before it dawned on her that even though she'd been told what was happenings he still believed Bryce to be dead and worst, to have betrayed her brother.

Bryce stepped closer to the group, searching his surroundings for any potential danger, always the Agent. Sarah looked over at him, not returning the giant smile he had on his face. She was still friends with Bryce, but she had mixed feelings about him. She knew Bryce the agent, accepted him for his flaws and strengths but once hearing about Bryce from college, the supposed real Bryce Larkin from before that CIA took complete control of him she wasn't so sure how she felt about him anymore.

She understood completely now that what he did to Chuck, getting him expelled from Stanford was to help Chuck but the way he did it and the effect it had on Chuck's life after had caused her opinion of him to change forever. And even though they now know he never slept with Chuck's girlfriend back then, the fact that he hadn't dispelled that earlier and let Chuck rot in his misery incensed her greatly.

In short, she didn't like Bryce Larkin anymore now that she thought about, and judging from the angered look that appeared on Ellies face once the shock of seeing him alive wore off, she wasn't the only one.

"Hey guys." Bryce said stepping up to them, hands in his coat pocket. "Ellie, it's nice to see you again." He flashed her a bright grin.

Ellie however stepped closer to him and pulled her arm back, making a fist and swung it right into Bryce's face. Bryce stepped back and fell from the punch and all Sarah and Casey could do was stand there and stare. The General however had an impatient look on her face.

"Ms. Bartowski, what on earth are you doing?" She said sternly. Ellie didn't looked ashamed at all, not taking her eyes off of Bryce.

"I'm sorry General, just some unfinished business, I'm finished now." She unclenched her fist and wrapped her arms around her herself.

Bryce picked himself off the ground, covering the eye that had just been hit, and tried to straighten himself out.

"Are you alright Agent Larkin?" Beckman asked him. He nodded he was.

"I know I deserve that for what I did to Chuck." He admitted. Ellie just rolled her eyes. "So what is going on with the Intersect that I had to be pulled off my assignment?"

Sarah took a deep breath and explained everything gain to him. His eyes were widening and eyes narrowing as she told her story to him. He was quiet for a few moments once she finished and in the back of her mind she was thinking that he believed her to be crazy too.

"So Chuck actually communicated to you though he was restrained and supposedly unconscious. He did it through a computer monitor?" Bryce questioned.

"Uh, yeah." Sarah said hesitantly, her heart lowering feeling like she was alone in this. Bryce was quiet for a few more moments.

"What was the set up? What kind of electronics were hooked around him aside from the ones monitoring his vitals?" He inquired. Sarah was startled.

"You believe me?" She asked shocked.

"Of course I do. Why wouldn't it?" Bryce asked her. Ellie glared at him.

"Well for one it sounds like something out of those movies Chuck watches'." She said crossly. Sarah's heart sank again, wishing that Ellie was on her side. Though she couldn't tell if she was like this because Bryce thought it was possible or because she truly believed it.

"Ellie the Intersect is a piece of technology that is years ahead of us. It's so advance that the only person able to handle it is Chuck. The fact that it's somehow learned to synthesize a life like robot, take control of an entire building, and set Chuck up in a way that he can communicate without speech well, I'm sure that's just the tip of what it can do. "He paused seeing how his speech had affected those around him. "This thing, can analyze and cross analyze anything and everything it's given. It's like having thousands of doctors doing trial and errors and processes. In theory anything is possible." He finished.

They were quiet for a moment each considering that thought and how scary it was. Suddenly the task seemed daunting and impossible. Sarah wasn't quite sure where to being to try and get Chuck back.

"Ok so we're ok agreement that Walker is on the level and that this thing has somehow come to life in a way and is keeping Bartowski prisoner?" Casey growled out impatiently. They all nodded. "Good, now we need a plan."

"That's going to be a hard task to accomplish with the Intersect able to lock into all electronic surveillance. It even broke through your Jammer Casey. And that was the best one out there." Sarah stated.

"Leave that to me. Meet me here in one hour; take off any and all electronic devices. Even ones you don't think would be a risk. If this thing has access to anything it wants via electronic communication we'll have to go old school." With that Casey turned to leave with a salute to the General and went off. Everyone stared after him a few moments in confusion.

"That is a very complicated man." Ellie stated simply to which everyone nodded their agreement.

A little over an hour later they were all crammed inside an old van Casey had driven onto the tarmac. It was a tight fit with all of them, including the General to their astonishment as they sat in the back. Casey had brought pads of paper, markers, tape, everything they needed to come up with a viable plan on what to do.

"Ok, where do we start? What do we know?" Sarah started, sitting back against the wall of the van cross-legged. General Beckman cleared her throat to get everyone's attention, sitting upon a crate as regally as possible.

"I know you are all concerned with Chuck Bartowski's safety, as am I, but I must stress the importance that the first objective of this mission must be the termination of the main Intersect computer." Everyone sat silently, already knowing that she would say that. She had to; she had the whole country to worry about.

"But my brother is in there." Ellie protested. Sarah smiled slightly next to her. She wanted to say the same thing but as an agent she had to follow her General, even though she knew that when push comes to shove, Chuck will be her first priority as well.

"I understand Dr. Bartowski. But if that thing gets any more freedom it can do a lot of damage to the defense of this country. I'm sorry folks but I can only allow a one hour window before I send fighters to destroy the building. It must be destroyed." She paused and looked at each of them. "You have one hour to plan and then put it into effect. I think it's best if I do not know what you are planning on doing. Let the guard know when you're leaving."

With that General Beckman stood up best she could and exited the Van. They watched her walk toward the plan briskly before closing the side door again.

"Well that was cheerful." Bryce said breaking the tension. Ellie shook her head angrily.

"That's it? That damn computer comes first? She'll sacrifice him for a fucking computer." She said getting angrier. Sarah placed a hand in hers and squeezed trying to calm her.

"She has to Ellie. That computer is dangerous. But don't worry we will do everything we can to get Chuck out. I'm not leaving without him." She said meeting Ellie's stare.

"And if we fail, he won't die alone. We will be with him." Casey declared. Ellie had tears falling out the corner of her eyes at the loyalty they showed. She knew Chuck had a tendency to rally people around him rather he realized this or not, but it always amazed her to see how much loyalty people actually had for him.

"Ok, so what do we do? How do we accomplish this?" She said wiping her tears away.

"Ellie, you're not in the 'we' you need to stay here or stay at home. This is too dangerous." Sarah protested.

"No. I'm going to save my brother. You guys can have your side mission of shutting that thing down but I'm going straight for Chuck. If we do it at the same time it saves time." Ellie said, looking around.

"Ellie, no…-"

"Actually Sarah it would be a good idea." Bryce interrupted. Sarah dropped her pen and glared at him, he had the good sense to looked slightly guilty.

"I don't think Chuck would want his sister in immediate danger. We don't exactly know what that thing is capable of on top of the time limit and the building will be blown up."

"Yeah but could be our best chance. Not only is she Chuck's sister but she's a doctor. A neurologist to be specific. The Intersect might just let her walk in and go to Chuck because of their relation. You said the Intersect took Chuck to protect him. Well killing his sister isn't protecting him. And if he is integrated into the system he'll know if she's is eliminated which would harm him." Bryce finished. He hadn't taken his eyes off Sarah's during the whole speech. She relented by breaking contact first.

"Casey, what do you think?" Ellie said quietly. They looked at him for his reply. He gave Sarah an apologetic look before answering.

"Sorry Walker but he's right. Ellie would be an asset on this mission." Sarah looked down at her paper unable to speak for a few moments.

"Fine, let's get planning then."

Bryce pulled out a paper schematic of the building and they looked over it. It was determined that they would need to turn off the generator on the fourth floor in order to cut power to the Intersect. While it was backed up on many generators in order to prevent tampering and in case of power failure, but it was little known, for a reason that by taking out that one generator it would knock out the entire system.

They decided to break up in two teams. Casey would be going with Bryce to destroy the generator and Sarah would be there to protect Ellie. Getting in to the building was another matter. Ellie and Sarah were to go through the front doors and get up through the elevator to see Chuck. Hopefully they'd be able to talk to get him to unlock the door down the secret staircase she had escaped through and let Bryce and Casey in.

Forty minutes later they existed the van and went on their way.

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sarah and Ellie stood outside the front doors of the innocuous building that was currently holding Chuck prisoner. Ellie had been eager to enter the building and make her way up to Chuck but Sarah held her back, telling her it's best to let the Intersect detect them first and see where it goes from there.

They stood there for a good five minutes before the doors opened on their own accord to welcome them in. Sarah took a deep breath before grabbing hold of Ellies hand and leading her into the building. The doors shut quickly behind them as they entered, the sounds of the locks clicking the only sound in the room.

Sarah looked around a moment, expecting the robot Chuck or some other machine to make its way to them to either kill them or lead them but nothing happened or appeared. She took the time to look at Ellie, who had a determined look upon her features even as she glanced around the room taking it all in.

"Come on. The elevator is this way." With that she leads Ellie down the hall and through a few turns before finally reaching the elevator at the end of the hall.

"Where is everyone?" Ellie said softly as Sarah pressed the button.

"We don't know. That's part of why we're here. Chuc—The Intersect just said that they were disposed of." The doors to the elevator opened then, empty and sterile looking as the last time she was here.

They walked into the box and turned around to face the door as it shut. Sarah reached over to the panel and was about to press in the key sequence code that would take them directly to the fourth floor, hoping that the system didn't lock the code out, but before she could touch the panel the elevator began moving.

"I hope this is a good sign." Sarah muttered quietly to Ellie who just nodded back. A few minutes later the doors opened on the fourth floor into the same room as before. They stepped off the elevator and Ellie stepped forward, mouth open eyes wide at the complexity of the room.

"Wow. Just, wow. This is amazing." She gasped.

"I'm glad you like it." A male voice said to the right of them. They both startled and looked, Sarah immediately drew her gun and Ellie's face went from one of awe to surprise.

"Oh my god Chuck!" She said going to take a step forward but Sarah stopped her.

"Ellie that's not Chuck. That's the Intersect." She said firmly, glaring slightly at the Chuck standing before her. He didn't show any emotion at that.

"She's right Ellie. I am not your brother. "He said softly. Ellie's face fell and she could feel prickles in the corner of her eye.

"Where is he?" She said softly looking around as if he would just pop out of nowhere.

"He is safe Ellie. You should leave." The fake Chuck walked closer to her and Sarah raised her gun directly to his head.

"Don't come near her. Just take us to Chuck." She demanded. The Chuck looked at her for a moment, his eyes going out of focus for a few seconds before coming back.

"Very well Agent Walker. Ellie, please follow me." He said before turning around and exiting the door behind him. They followed behind giving a small distance between them. He lead them down the same path across the huge white room to the same door that he had lead Sarah to the day before. He stepped in front of the panel and placed his hand on it letting the door open.

Ellie was eager to see her brother and waited impatiently for the doors to open. She looked once at the Chuck by the door finally entering as he gave a slight nod with his head. She entered the room eagerly seeking out her brother.

"Chuck!" She shouted when she finally saw him. She rushed to the center of the room to him and looked over him visually before physically.

Sarah followed at a more sedate pace, taking more time than she did before to look around the room. She looked to the left and saw Lupo, the tiny robot idly sitting at the end of the platform that Chuck rested on. It chirped once, and blinked a light as if letting her know he acknowledged her.

"What have you done to him?" Ellie asked not turning around. The Chuck walked past Sarah and up to the platform next to Ellie and looked down at his human model.

"We have done nothing to harm him Ellie. He lives well. He dreams." He said simply. The mechanical detached way of The Chuck's way of talking was starting to unnerve her. She couldn't believe that she had lived with him for two months without fully knowing something was off.

"What does he dream about?" She asked curiously seeing his eyes move back and forth under his closed lids.

"Of Sarah mostly. Of you too. He fears you will marry and create your own family, leaving him behind." He said sadly finally looking at her again. She looked him right in the eyes, trying to give a hard look but found it difficult staring into the soft brown eyes that were her brothers.

"That would never happen. They're just dreams. They don't mean anything." She said firmly.

"They mean something to him. Whether it's the truth or not will remain to be seen. But he is safe here, I promise."

"You have no right to make promises to me." She said angrily turning completely to him.

"I am part of your brother Ellie. You are part of me." He said simply. To Sarah's surprise Ellie laughed.

"No, you are not part of my brother. You stole his appearance and you stole his life but that does not make you Chuck Bartowski in any ways shape, form or percent. If I cut you now you will not bleed blood you will just spray antifreeze all over the place and make a mess. Don't you dare speak for him?" She said in a low hiss right in his face. The Chuck didn't blink or show any reaction whatsoever, which unnerved her greatly but she refused to step back.

Finally he gave a nod and turned away, stepping down from the platform. He walked passed Sarah and toward the door before finally turning backing to Ellie.

"That very well be Ellie, but regardless, Chuck Bartowski will not be going anywhere. He will remain here. And you will stay here with him." He said simply. Ellies eyes narrowed at that.

"And what about Sarah?" She asked, not taking her eyes off The Chuck. He however looked directly at Sarah.

"That will be determined." With that he turned away from them existing the door. They heard the metallic sounds of the doors locking.

They stood in silence for a moment just staring at the door; half expecting him to come right back. Sarah felt a small tug on her pant leg and looked down. Lupo was tugging on the leg for her attention and she couldn't help but smile at the tiny thing, thinking it was almost cute. But it broke her from her thoughts as she quickly marched up to the platform next to Ellie.

She looked down at Chuck, not seeing any change from the previous day. He was still pale and still except for his eyes that moved rapidly in sleep. She gently ran her fingers through his curly hair, allowing a small smile to grace her lips as she did so. Ellie immediately began taking stock of everything attached to him and trying to figure out what each did.

"I think the electrodes are directly implanted into his head." Sarah whispered to Ellie, still running her fingers in his hair. She removed them for a few moments while Ellie ran hers through feeling the electrodes protruding from the skin.

"Yeah. It's really advanced technology. That must be how they are able to interface with him." She replied back. Sarah leaned closer to Chuck's ear hoping she'd be able to reach him.

"Chuck." She said softly. His heart monitor sped up a bit at hearing her voice. "Chuck, can you hear me?"

"Sarah…" Ellie said quietly patting her shoulder to get her attention. Sarah looked up at her and Ellie pointed to the screen directly across from them, the same one Chuck used yesterday to communicate with her.

"I can hear you Sarah." The words said. Ellie let out a sob and covered her mouth with her hand. Sarah brushed the side of his face as his eyes opened and stared blankly at the ceiling again.

"Oh god, Chuck." Ellie sobbed.

"I'm ok Ellie" The screen said before going blank again.

"No Chuck. You're not ok. Not till we get you out of here." She said.

"Chuck, how much control do you have over anything here?" Sarah whispered to him, watching the screen. It was blank for a moment before lighting up again.

"What do you need?" It said.

"The door at the bottom of that staircase. Can you open it?" She asked.

Nothing happened for several minutes and Sarah was afraid they had lost the connection to Chuck. She continually looked down at his face before going back to the screen. Ellie had taken to rubbing his arm partly encouraging and partly because it was so cold.

"Casey and Bryce are down stairs. Doors unlocked. They will be here soon." The screen finally lit up. Sarah let out the breath she was holding relieved. She placed a kiss on his forehead.

They stood in silence while they waited for Bryce and Casey to come up the stairs. Ellie walked around the machines examining them, looking at their function and determining if it will be safe to disconnect them. Finally the other two came to the room and hesitantly came in the room. Both looked around it amazed at all the electronics and robots around. Casey stopped suddenly as Lupo rolled in front of him holding up his hand.

"What the…." He started to say and pointed his gun.

"Casey no!" Sarah said harshly stopping him from blowing the little robot to bits. "That's Lupo, he's on outside." She said simply as Casey gave her an incredulous look. Bryce bent down to examine it a moment before finally approaching the three.

"You named a robot? Geez Walker, going soft?" He said sarcastically. Sarah rolled her eyes at him not dignifying it with an answer.

Bryce stared at Chuck and the machines stunned. It was such an intricate set up. He could see the wires hooked up to Chuck and he watched as he walked around to stand by Sarah as they moved and changed in accordance to their function.

"Oh my…I'm so sorry Chuck. I never wanted this for you when I sent you the Intersect." He whispered to his former friend.

"This isn't your fault Bryce." The screen lit up startling Bryce to nearly falling off the platform. The words deleted before adding a 'This Time' to it.

Sarah laughed for a second before reaching her hand to steady him. Ellie however agreed with her brother and refused to give anything to Bryce so she continued focusing on the machines.

"I think it's safe to detach him from all this. I don't think it'll cause too much harm but we'll need to help him out. This tube is feeding him some sort of sedative which is what's keeping him immobile but still able obviously to use his mind." Ellie stated finally.

"Ok then let's start-"

"Not yet Sarah." Bryce said interrupting her. He grabbed her hand from where she was about to pull a wire from him preventing him.

"He's been like this for two months Bryce we need to get him out of here." She said angrily. He gave her a look before letting go of his hand.

"I know but if we detach him now it might send off some alarms. We need him so we can destroy the generator." He explained. "We still have to destroy the Intersect."

"Guys should we really be walking about this here, I mean…isn't the Intersect a see all?" Ellie pointed out looking around the room. The robots and machines continued to ignore them and work on their tasks.

"It's safe." The screen lit up. Bryce quirked his brow.

"How?" He asked simply. But Chuck offered no answer. "Ok fine. So how do we get to the generator from here? From the schematics it's behind the console in the main room."

"Which is behind that door." Sarah said pointing. "And I'm pretty sure the other Chuck is out there."

"So we go in there and blast the crap out of him to get behind the console." Casey said, getting annoyed and looking at his watch. They had just over half an hour left.

"Follow Lupo." The screen said. They looked over to where Casey stood and Lupo stood by his feet still.

"This thing?" Casey said with disgust. The screen began blinking rapidly with the same words and finally Casey relented.

The little robot led them to the other side of the room and pointed to be picked up. Casey refused to touch it so Bryce stooped down to get it, laughing slightly as the wheels tickled his hands. He moved it over to a console by the door and it used its little pointer arms to press in buttons till the door opened. With one last glance they walked into the doorway, with it closing behind them.

"This might sound a little weird but I kind of want that robot." Sarah said to Ellie who grinned at her.

It had been ten minutes of them just staring at the machines around them; Chuck had closed his eyes once more putting on an air of sleep. Sarah wanted to talk to him more but Ellie convinced her that it might be wise to let him rest while he can till they get him out. Though she wasn't entirely sure if he was sleeping.

Suddenly Chuck's eyes opened wide starting Sarah. His heart rate when up and Sarah looked at the screen waiting for whatever he had to tell them.

"He's coming." It said simply. Sarah's heart beat faster, knowing who he meant but needing confirmation.

"Who's coming Chuck?" She said softly.

"Him." It said simply.

Sarah turned around quickly at the sound of the locks clicking. She saw The Chuck enter the room an angry look upon his face that looked so unnatural on her Chucks face.

"What have you done?" He said angrily approaching her. She stood up straighter, in full agent mode now. She signaled for Ellie to stay where she was.

"I have no idea what you mean." She said as he stepped right up to her, towering over her shorter frame.

"There is no communication to this room. It's been cut. What have you done?" He demanded low and deadly. She just stared right back not giving anything away. The Chuck glanced over to Ellie seeing her fear before looking back to Sarah's hard look. He raised his hand and backhanded her hard across the right side of her face.

Sarah stumbled to the left and landed on top of Chuck's legs. She stayed there for a moment getting her baring's before reaching her hand across her mouth tasting blood from the split lip. She stood up straight looking at him defiantly.

"Now you shouldn't have done that." She said back to him with a slight smile. With that she drew her arm back and punched him in the face causing him to stumble before twirling and kicking him in the stomach.

"Sarah away from the bed!" Ellie screeched as The Chuck came after her once he recovered.

Sarah jumped off the platform as he ran at her side kicking her, she blocked his foot and grabbed it causing him to twist and kick her in the head with his other foot. She stumbled for a moment getting back up and flying at him with punched and kicks.

They fought hard but Sarah was tiring. He wasn't a human with weak points to making him weaker. He was a machine and it felt like a losing battle. Finally getting her head back in order she reached for her gun and pointed it straight at his head pulling the trigger. Chuck stumbled for a moment shaking his head before coming at her again. Her eyes widened and she shot another few rounds at him but he wouldn't stop.

She backed up against the wall and close to it as possible and shot another few rounds but nothing seemed to stop him. She had honestly never been so scared in her life. She dropped her now empty gun, not bothering to reload with her extra clip and got ready for another physical battle even though she didn't think she could hold out for much longer.

He was just a few feet away from her, sparks flying form him, his synthetic skin peeling off in some places showing the machine below it. She was disgusted at the sight of it and terrified as well.

Just before he reached The Chuck stopped and stood up straight. She got in the beginning stance ready for whatever physical attack he threw at her but none came. His eyes went distant like they had so many times over the course of two months but they never refocused, just kept staring at nothing. She relaxed her stance just a little, enough to release some tension but still ready in case he changed again, but a few minutes later The Chuck collapsed into a heap on the floor.

Sarah stared down at it stunned and unexpected. She wasn't quite sure what had happened. She looked over at Ellie who was staring out at her in horror.

"Sarah are you alright?" She shouted at her. Sarah just nodded and looked down at the heap of Chuck. She made her way over to Ellie looking at Chuck and wondering what happened.

"Chuck stopped him. Your gunfire weakened his connection to the main Intersect and he was able to gain control enough to stop him. I think, from what I read." Sarah looked down at Chuck whose eyes were wide open again.

"Thank you Chuck." She said softly. There was no trace but she swore she could feel him smile.

"No problem." The screen read.

A few minutes later the power fluctuated and a loud humming sound happened before everything went dark before soft green lights filled the room from the emergency lights. The hums and whistles continued as the machines around them powered down, the robots stopping in the middle of their tasks, the lights on the consoles going black.

Sarah and Ellie looked at Chuck's form, all the machines turned off. Ellie panicked for a moment, pressing her fingers against his neck and was relieved to feel a strong pulse.

"He's alive, and fine I presume. Like I said it gave him some kind of sedative paralyzing cocktail mix so that's why he can't move. We'll do a tox screen once we get him to the hospital." She said reassuring herself as well as Sarah.

They turned towards the door as they heard footsteps and watched Bryce and Casey walk into the room both looking banged up and dirty.

"What happened to you guys?" Sarah asked alarmed. Casey grunted at her.

"Stupid robots attacked us. Luckily they powered down once dismantled the generator." Casey said. Sarah looked over and saw Bryce holding something in his hands. She reached out for it and he gave her the body of Lupo.

"I wasn't sure if we were to save him or not but I couldn't leave the little fella there." Bryce said sadly, petting the robot now in Sarah's arms. Casey rolled his eyes and walked away muttering about having to call General Beckman.

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"Three Days Later"

Chuck Bartowski laid in bed relaxing. His eyes still felt heavy and he felt very fatigued from being sedated for so long but he felt good at least being able to finally move when he needed to. Especially since he had to itch his nose for a month. He closed his eyes and relaxed further into the pillow behind his head and sighed contently dozing off until a light tap at the door woke him up again.

"Come in." He said softly, his voice hoarse from lack of use. He wanted to turn over to face the entrant but decided to wait to see who it was first. The scent of oranges hit his senses as light footsteps entered and closed the door behind them. He rolled over then and sleepily looked up at Sarah.

She smiled down at him for a moment before looking around the darkened room. It was past noon and the sun was high and bright, filtering in through the cracked curtains. She looked at Chuck again for a moment before deciding against opening the curtains even though he was in desperate need of some sun.

"Hey you." She said softly to him.

"Hey yourself what's up lovely lady?" He replied. She leaned on the bed and crawled over him to get to the other side. He groaned as she did so faking massive pain.

"Knock it off Chuck." She said smacking his arm as she lay down on her side facing him.

"You could have gone around you know instead of wounding the injured. That's very inhumane of you." He chided trying to keep a serious expression on. He failed and laughed at her eyes rolling.

"So, tell me, how did this all happen." She said laying back and staring at the ceiling. He had debriefed with the general once he woke up in the hospital but had yet to give his full account, not that there was much to tell since he was unconscious for most of two months, or at least stuck within himself, something he hopped to never feel again.

"I honestly don't know Sarah. I went for that install and next thing I know I can't move." He said softly his eyes going distant. Sarah hated when his eyes did that now, reminding her of the robot Chuck, but she allowed him his moment.

"That must have been frightening." She whispered back to him. His eyes focused again much to relief.

"Honestly Sarah it was the scariest thing I've ever experienced and I never want to do it again. I can't even explain the terror of being awake and not being able to move." She said. She nodded her understanding. Not really having felt it herself but she could imagine the horror of losing complete control like that.

"How were you able to control any part of the computer? That's an amazing feat. That technology was just amazing." She turned to her side resting her head on her hand and looked down at Chuck. His eyes were closed and after a few moments she thought he had fallen asleep again.

"Honestly I don't know. I felt Lupo communicate with me. I can't even explain how or what. It wasn't in words or images. I saw and heard nothing but I could communicate with him. He wasn't like the other robots; I could tell that right off. "

"How could the Intersect create something different from everything else it did?" She asked confused. The whole Lupo thing a mystery to her after seeing the other robots. Chuck thought for a few moments before finally answering.

"Well like the Intersect, it's a computer. It was given commands, options, parameters and it evolved. I guess like humans, robots just evolve the same way with the codes. Each robot was given different coding, parameters whatever and somehow Lupo ended up being what he is. I don't think we'll ever find out." Chuck explained. None of what he said made sense to Sarah but as long as Chuck understood that was all she needed.

"Why Lupo for the name?" She asked curiously. Chuck smiled at her at that.

"Because he makes a 'lup lup' type sound so I called him Lupo and he liked it." Sarah laughed a real hearty laugh for the first time in a while.

The whole situation was scary. The 48 hours she had spent from finding out the Chuck that was with them was actually not Chuck to getting to the hospital after the Intersect was shut down was some of the most terrifying times of her life. And that's saying something.

"They took apart the Intersect. They disabled everything and put explosives around the building and blew it up. They'll be hauling the pieces out for the next week for further destruction." She told him, knowing he would be curious on what happened to the machine. He didn't say anything for a few moments.

"Did they find what happened to the technicians?" He asked. She didn't want to tell him, knowing how he valued every human life but he should be told.

"Yeah, they found them all in the basement. They had been killed. The only people who are left that's gone in that building is us and a few others. Everyone else is dead." She stated.

"That's so sad. I feel sorry for those people's families. They just wanted to be a part of something amazing."

"The Intersect put a huge dent on espionage and terrorism while it was still up, and we still have the data. But for now. They decided to just keep you." She went quiet then laying her head back down on the pillow and still staring at him.

She moved her hand near his face and traced his features with the tip of her fingers. Chuck closed his eyes at the feel of them, trying hard not to shudder in pleasure at the touch. Their moment was interrupted by another knock at the door however. Chuck sighed and opened his eyes.

Ellie came in slowly noting Chuck and Sarah laying on the bed. She tried to contain a smile as she lifted something from the floor.

"Lupo!" Sarah cried out excitedly sitting up. The little machine made a whirling buzzing sound before he made the infamous lup noise." Chuck rolled to his back and sat up a bit holding his arm out for the machine.

"Yeah, I fixed him. He just needed his own power supply, huh little fella?" He petted the silver robot causing Ellie to laugh.

"Yes just be sure to pick up after him and don't forget to feed and walk him." She said sternly in her best motherly tone.

"Pick up after him? He wouldn't make a mess would you Lupo?" He asked it. Lupo made his lup noise but Ellie just rolled her eyes. You can see the mess he made in the kitchen getting juice from the fridge. He built a tower and was climbing on it. "

"Why would a robot need juice?" Sarah asked confused. Chuck just grinned.

"I think it was getting it for Chuckles here." Ellie replied before exiting the room and closing the door. They were silent for a few moments just sitting and playing with the robot.

"So what happens now?" He asked her finally. Sarah thought about her answer, trying to find the best way of saying it.

"Right now you're the only Intersect and they're going to keep it that way for a while. So for now, we just go back to the way we were before the computer was built. We go back to normal. The Orange Orange, Buy More, missions. You know." Chuck smiled at her.

"Yes, at least we have Ellie to patch me up now."

"Thank goodness, because it's getting harder to explain your accidents. If you would only stay in the damn car….."

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The End

A/N: Hope you enjoyed it. Was just something i worked on while i worked on the other story. I'm currently working on kind of one shots to be put with the story. All reviews appreciated. Enjoy!