A/N: YAY! I have me a Beta! Thank you charahkids!

Chapter 2

Confusion was the first thing that Chuck felt when he awoke the next morning. He opened his eyes slowly, blinking several times to adjust to the light filtering into his room before he was able to fully open them. The first thing he saw was his Tron poster, hanging on the wall like it had for many years. He stared at it for several minutes, letting his mind try to wonder on how he came to be in his room.

After several minutes he took a deep breath and turned onto his back, watching his room rotate with him as he turned. Everything looked the same as it did when he left it last time except the light from his window was definitely morning instead of midafternoon.

Chuck closed his eyes again and focused on breathing. After counting to ten he finally pieced together what he remembered starting with the afternoon, the last time he had been in his room, or their room. A small smile crossed his face at that correction, thinking of the room that had been his for over ten years as no longer just his but theirs, the room he shared with the one he loved.

Brining his mind back to focus, last he remembered he was getting dressed after an afternoon session of expressing love to Sarah. They were supposed to meet Casey in the courtyard in ten minutes to go to the CIA facility where he was to receive yet another update for the Intersect. They had been discussing asking Beckman for a small reprieve before the next update. He'd had five in the last two weeks and the intense violation of having data stored into his mind was beginning to take a toll on him physically and mentally as well as the stress on the team as they still had missions.

Sarah expressed her concern for his wellbeing and he agreed with her and had promised with one last passionate kiss before they exited the room that he would speak to Beckman as soon as he could about it.

The drive over to the facility had been silent for the most part, the beginnings of a migraine already starting to stretch through his entire head and down his neck. He tried not to show any pain and just smile at Sarah, holding her hand tightly in his. He was feeling tired, exhausted really. They had a late night mission that lasted into the early morning. Both Sarah and Chuck had come home, took a quick shower that involved much to his dismay just showering and crashed half hazard onto the bed.

By the time they got to the facility the migraine had been in full force and Chuck had a hard time even walking. He held tightly to Sarah noting the concern on her face and tried to smile at her to reassure her. He wasn't even paying attention to what went on around him until suddenly Sarah wasn't holding his hand and was instead assaulting a technician in front of him.

After a moment shock he pulled his wits about and called her off, telling her it was alright. The chair that sat in front of the Intersect computer did look quite frightening and memories from the mission in the suburbs came to mind. It took a lot of will power not to flinch away and fight back when they went to pry his eyes open, but he knew it was necessary. He was so tired and worn, the pain in his head already too great that he wasn't quite sure he would be able to keep his eyes open on his own anyways.

That was all he could remember until now. The lights went off; the screens came on and then nothing till now.

Chuck stared at the ceiling of the bedroom for another few moments, trying to see if he could assemble some kind of memory, even if it's fragmented on what happened between then and now. But there was nothing, his mind was completely blank.

He turned his head to the left, expecting to see Sarah there though not really surprised not to. Based off the suns position coming in his room he'd say it was mid-morning and Sarah while not really a morning person would be up by now checking reports or doing a workout. He laid there for several minutes before finally pulling the blankets off him and sitting up.

His head spun as he sat at the side of his bed causing his eyes to close tightly. He felt bile rise in his throat and he tensed himself to force himself not to throw up. He wondered idly if perhaps his lack of memory had anything to do with drinking the previous night. He knew that Morgan was getting kind of that he and Chuck haven't been able to hang out much recently, and drinking would be something he would agree to if it made his little buddy happy. However remembering the update and the migraine before he doubted that was it.

After a few moments he was finally able to feel himself stabilize and he opened his eyes slowly once again to look around. He noticed his glass of water he typically had on his bedside table for bed sitting there and he reached out and grabbed. He hungrily drank the water down, reveling in the cool liquid as it slid down his throat. He drank the whole thing down, coughing as he finished it from drinking too fast. He set the glass down on the nightstand again and covered his mouth and tried to quail the coughs.

At last they settled down Chuck took one final moment before finally trying to stand. He felt unsteady on his feet but still placed one foot in front of the other till he was using his arm to lean against the side of the door. He took the second there to look down at his What's this about Sarah?s, noting he was in his pajama bottoms and a sleep shirt. He couldn't remember changing his clothe, but they were on straight enough that he figured he must have put them on.

His feet feeling steady he opened the door slowly and walked out. He could smell coffee coming from the kitchen and walked in that direction, letting it lead him. He was never really any good unless he had at least one cup of coffee. Chuck was always ashamed that he had become one of 'them'. Them being the people of the world dependent on a morning dose of caffeine to get started, but with his odd shifts and jobs in the past three years he's needed that boost in the morning.

Reaching into the cupboard once he reached the kitchen he immediately poured himself a large cup, bringing it up to just under his nose. He smiled at the cup as whatever nausea and cobwebs he felt washed away with the delicious smell of the bitter coffee. Taking a sip he took that opportunity to search his memory again only to come up blank.

"Good morning Chuck." Sarah said startling him as she came up behind him wrapping her arms around his waist. He jumped slightly but thankfully didn't spill any of his precious coffee on the counter or worst, himself.

He set the coffee cup down, albeit a little reluctantly and turned around in her arms and smiled at her. Hunching down slightly he captured her lips with his and gave her a soft kiss, wrapping his own arms around her. Pulling back a few seconds later he stared down at her with a grin on his face.

"Good morning to you Sarah." He said lovingly. She stepped up on her toes to place a couple kisses on his jaw before pulling back slightly, he felt a shiver run from the spots where her lips touched him down through his body.

"Are you feeling any better today?" She asked him. He felt a loss against him as she lowered her arms and grabbed his coffee from behind him. He wanted to hold her longer but instead followed her, with his coffee into the living room.

Sarah stood in front of the couch waiting for him to catch up and for him to sit first before handing his cup back to him and sitting down next to him. He wrapped his arm around her shoulder as she snuggled into his side. He took another drink of his coffee as he relaxed into the couch and enjoyed the moment.

"Well, are you?" Sarah pressed a few minutes later, breaking the silence.

"I'm fine Sarah. Healthy as a horse. Whatever that means." He joked giving her another smile. He placed a tender kiss on her crown and looked down at her.

"I'm glad. That update was rather brutal. You were so sick." She commented embracing him, burying her face into his chest.

"Well the good news is I don't remember a thing, so there's that." He joked. He felt Sarah's eye narrow in his chest before she pulled back to look at him confused. "What?"

"Nothing at all?" She asked him confused. Chuck thought one last time, his mind zooming back through all the memories of yesterday. Nothing stuck after the update started.

"Not a thing Sarah. What's wrong?" He asked her feeling slightly alarmed. He was prone to worry so the feeling is not foreign to him, however seeing worry appear on Sarah's face always brought it up a notch being as she's a superspy trained to hide her emotions.

"It's just, nothing? At all? you don't remember the ride back or getting ready for bed or anything?" She asked him searchingly pulling back further from him.

"I swear last thing I remember is the update starting. How did we get home? Did Casey carry me?" He asked her feeling dread in his stomach. If Casey carried him home and had to help him get ready for bed he would never hear the end of it. The man held grudges like no one else in the world Chuck knew.

Sarah didn't answer him, instead her eyes looked over his shoulder slightly glazed as in thought. He wanted to press her more about what was wrong but he'd learned long ago that pressing Sarah for information was useless. He would just have to wait and wonder until she was ready to give information freely.

"After the other updates, did you miss any time?" She asked him after a while. Chuck thought for a moment, back to those updates. All he could remember was pain afterwords and lying securely in Sarah's arms as the dizziness passed after he woke up. Aside from the time the update started and waking up then he didn't think he missed anything.

"Not that I know of. What's this about Sarah? You're starting to freak me out." He admitted to her. He watched her intently as she went through some internal struggle for several minutes before she finally looked up to him and gave her best megawatt smile. Normally anything and everything would disappear from his mind when she gave him that smile but he felt some sort of foreboding.

"It's nothing Chuck. Don't worry about it." She told him, kissing him. He was about to protest but as always kissing Sarah filled him mind with rose petals and music, disrupting any other thought from creeping into his head. "We better go, Beckman wants a briefing." She said pulling away from him causing him to groan.

"Can't we just blow her off and stay here? I feel sick." He said giving her the puppy dog pout he could, but her alarmed look at that wiped it right off his face.

"You said you were fine. Are you sick? What's wrong?" She asked alarmed pressing her warm hands onto his face. He loved the feel of them, but he grabbed them from him and brought her palm to his lips placing a kiss on it.

"I am fine, I'm joking. I just want to stay here with you." He told her lovingly, brushing back some of her hair from her face. Her expression flickered from concerned to annoyed then finally on impassive in a blink of an eye. He made a silent note to himself not to play sick anytime soon.

"That's not funny Chuck. Now go get dressed." She said firmly standing up and away from him. He wanted nothing more than to pull her down back on the couch with him to snuggle more but the determined look on her face prevented him.

With a final sigh he drained the remaining coffee from his cup and stood up to go back to his bedroom to get ready.

The ride to Castle was silent. Once he was showered and dressed Chuck came back out to the living room to see Sarah standing in practically the same spot he had left her, though this time her phone was in her hand and she seemed to be texting.

He grabbed his keys from the bowl by the door but Sarah quickly took them away stating in a tone that left no room for argument that she would be driving and walked out the door and waited for Chuck to follow before quickly closing and locking it.

That was the last words she said to him as they got in her Porsche and started driving towards Castle. He wasn't quite sure what he did wrong, if he did anything wrong. He spent the trip reviewing everything that they had talked about, everything going fine until he made the joke about being sick. Obviously she didn't like that and he wasn't sure why she took it so personally.

He opened his mouth several times to try to say something but nothing came out as they zoomed down the street. She turned hard cutting off another car causing Chuck to grab hold of the door as she barreled through the intersection and into the parking lot of the plaza where the Buy More sat and parked the car.

They sat there for several moments, Chuck trying to get his breath back as Sarah stopped the car and took off her seat belt. They sat in silence for several moments lost in their own thoughts.

"Sarah I-"

"It's fine Chuck." She said cutting him off. He frowned for a second before turning his body, best he could to face her.

"It's not fine when you're mad at me." He told her earnestly. Sarah gave him a sad smile back before turning to look out her window for a second.

"I'm not mad at you Chuck. I'm just concerned. "She admitted.

"About what Sarah?" He asked but got no response. "Sarah, please, talk to me. I know you don't like to but we have to talk about you know, stuff otherwise we get into trouble." She looked at him then eyes narrowed in confusion.

"What do you mean trouble?" She questioned causing Chuck to give a patient sigh.

This was always the hardest part of their relationship he felt, but he was always determined to do it. Chuck had grown up with Ellie raising him, Ellie being an emotional person to begin with and taught him it's better to talk about ones feelings then letting them fester, or something like that.

It had started soon after their mom had left them and Chuck was having a hard time dealing with it. He had changed and become more secretive and quiet, not wanting to put more pressure on her or their father from the stress they already had. It had gone on for several months until Ellie got ahold of Chuck's report card and saw his grades slipping.

"We can't do this Chuck. If you need help or having trouble with things you have to tell me." She had pleaded with him that same afternoon. Chuck had felt guilty that he had let it get so bad.

"I just don't want to be a burden." He told her sadly, curled up in a corner of his bed. She had wrapped her arms tightly around him embracing him. He felt warm and safe, the safest he felt since their mother had left.

"Chuck, you are not nor will you ever be. At least not to me. But we have to fight against out nature and talk about things. We have to be a team, and that means no keeping secrets, reaching out when the other needs help. I don't know what I'm doing. I'm just a kid too." She had pleaded with him. And he took it to heart. Since then up until the Intersect came into his life Ellie had been his confidant and he always told her everything.

Dating Sarah, loving her was the complete opposite of how he was raise. She was taught to keep her feelings to herself, not to talk about anything. Keep face that everything was fine. Communication was not her strongest point and he knew that going in, and he loves her despite that.

"What do you mean trouble?" Her voice echoed bringing him back into the present.

"I mean, like, communication wise. We let the unsaid fester and then it gets blown out of proportion." He said desperately, not wanting her to be any angrier with him. "You say you aren't mad at me but your actions state you are, and I just don't understand or know what to do." He admitted.

He watched as her features softened from annoyed confusion to understanding and love. She reached her hand out to him and Chuck held on tightly to it like a lifeline.

"I'm not mad at you Chuck, I promise. I'm just, really concerned." She told him. He heart slowed down from the pounding he hadn't realized it was doing in anxiety. He was relieved to hear that.

"What's there to be concerned about Sarah? I'm fine." He reassured her, holding his hand to his chest. He gave her his best grin trying to settle any insecurity she may be having, but she just shook her head.

"No you're not Chuck. These updates are…" She didn't finish and he knew what she was trying to say. They were hard and violent. Nobody knew that better then him.

"I know Sarah. But there's only one more of this set. After we'll just have to be more firm with the General about them. That they need to be further apart. Ok?" He told her softly. She nodded her agreement before leaning over the middle and kissing him. Chuck pressed into her best he could in the small car, wanting to get as close as possible to her, forgetting that they were in the middle of the plaza barking lot. He was starting to really get into it, running his fingers into her hair when a loud knock at the window on her side startled them both apart.

They jumped apart slightly, both out of breath as they looked over to the driver's side window to see Casey standing there in his Buy More green polo shirt with a grimace.

"Are you going to attend the ing or are you just going to do the horizontal mambo in public?" He growled out. Sarah nodded her understand and he walked off with a roll of his eyes.

They took a second to get their breath back before finally making eye contact. The disarray of their clothes and hair caused them both to laugh, breaking the passion that had been permeating the air. They took a moment to fix themselves up before finally exiting the car and entering the Orange Orange to get into Castle.

Director Jordan of the CIA read the report he had been sent by Dr. Krinshaw once again. He was excited by this latest development and couldn't wait to test it out. If it worked it would be a huge step for the US intelligence community.

He thought again for the hundredth time if perhaps he should share this information with General Diane Beckman. It had been determined that while it is a joint NSA/CIA operation the little NSA General would take point and tend to whatever was needed.

Director Jordan did not like that.

Sure he got daily reports of the activities of the team but he felt like he was out of the loop on it and all attempts to get into the inner fold had been shot down with the Joint Chiefs, citing that the Intersect was precarious and didn't trust other government officials easily. Considering the instability of it, they were worried that any change could cause the Intersect to stop working.

Director Jordan grinned thinking about that, reading his report. With this latest upgrade it would no longer be an issue. They will have their Intersect and it will work perfect without any pesky human emotions or whatever issues Bartowski had that would stop it from working properly.

He had informed General Beckman it was just an update, a large one needing to be done in a series of six steps. He wondered if perhaps he should tell her of the upgrade instead but decided against it. She'll be pleased with the results soon enough.

A/N: Dude, so sorry it's taken so long. I caught this nasty cold bug so all I've done since Monday is lay in bed and watch my new Chuck blurays. you should have seen my hair this morning, dude, note to self: Just because you're sick doesn't mean you don't brush your hair. *facepalm*