A/N: Okay people this is my first chuck fic. It starts just after season 2, why? Because I don't like were there going with season 3 ATM and i think i can do better. :P

I have a rough idea on what's going to happen from here on out but i'm just going to be playing it by ear. Basically i'm just going to go with were my gut takes me, but there WILL be:

- Charah

-Chuck won't start changing in personality and turn into a Bryce, just be chuck with SUPER KUNG FU GOODNESS!

-Casey will start being more of a mentor to chuck, only a bit though

-And they will actually start getting some help and respect from Beckman, which will be obvious from this Chapter.

-There WILL be Shaw bashing, if I let him show up at all.

I must insist that you rewatch episodes 2.20, 2.21 and 2.22 before reading this, or at least 2.22. Otherwise it might seem that I rush into their relationship a bit quick.

Updates are unknown but as often as I can with my new course, hopefully i won't be leaving you with massive cliff hangers but I hope you can stick around to read and not hate me

Thanks to BillatWork for the Beta, anything good in here is thanks to him, the crap bits are me.

Well enough of my ramblings let's get on with the show! I mean fic.... whatever :P

-Chapter 1-The beginning-

Chuck's room: 0900 hours

Chuck was laying down on his bed face first. He hurt all over, the flash of Kung fu had stressed his muscles. He was going to need to train physically so it didn't take such a toll. He thought of what had happened of the last 24 hours.

He'd given Ellie and Awesome a wedding on the beach, watched his on again off again friend die in front of his eyes and after finally being freed from the intersect deciding he would be the hero and download the new intersect into his skull before destroying any trace of the first copy. He had then flashed and taken down 5 members of the Ring in a matter of seconds.

But if that wasn't enough, he had gone through what seemed like an interrogation because of his actions, before being sent home with Casey and Sarah, who hadn't spoken to him the whole trip back. In fact he hadn't seen either of them since they got back.

He sighed into his pillow, why'd he have to be such a hero? The door cracked open causing him to open an eye to see it was, Ellie and Awesome weren't supposed to be back for a week.

"Hey there Moron. Shouldn't you be playing video games or something?" Casey said in his usual gruff tone, although some layer of concern was audible.

"What are you doing here Casey?" Chuck sighed.

"Just thought I'd come check up on you idiot."

"Don't you have surveillance equipment for that?"

"We weren't expecting to have to keep an eye on you after this."

Chuck didn't move from his position on the bed as Casey moved across the room.

"So what are you so miserable about?" Casey asked with a grunt.

"I'm not miserable Casey. I'm just sore and exhausted after everything that happened." Chuck said flatly. The room was quiet for a few seconds as Casey fidgeted, obviously struggling to figure out how to say something.

"What is it Casey?" Chuck asked in a slightly annoyed tone.

"Shut up moron. I was just going to say that what you did yesterday... With the new intersect... Well that took some balls. And thanks for saving our asses." He forced out. Chuck was shocked and sat up; he looked at Casey like he had grown a second head. Casey just tried to avoid his gaze.

"What idiot?" he said with a growl.

"I just... never thought... well thanks." Chuck stammered, blown away by Casey's praise.

"Well don't get used to it." He said angrily before walking out of the room. Chuck let out a small chuckle, even if Casey was being surprisingly nice, he was still Casey. His stomach grumbled in complaint, it wanted food.

-

Castle: 0930 hours

Sarah was pacing, and chewing her fingernails. She was extremely nervous. The large flat screen TV mounted on the wall flashed to life.

"Agent Walker." General Beckman said flatly, who looked down at Sarah through the small glasses on the tip of her nose. She had stopped pacing and was now facing the General with a focused look in her eye.

"General. What's going on?" Sarah asked sternly.

"Is my information wrong, and you haven't already been briefed?" she quizzed.

"No that's not it, there's... I..." 'Calm down Sarah' she thought. She took a deep breath, "General Beckman, I just received orders from the new CIA Director that I was to bring Chuck into custody at any means necessary without the knowledge of the NSA."

"Walker. It seems that you may not be following orders, seeing as I now know." Beckman warned. Even though Sarah was ignoring a direct order, she was still technically in the right because NSA was to have shared knowledge of all goings on with the Intersect. Although it still didn't mean she wouldn't be punished in private.

"I understand General. But I don't think this is fair on Chuck." Sarah was being quite bold. That was because after receiving her new orders, she had finally been pushed over the edge and decided enough was enough. After the wedding she had decided that she was going to start standing up for what she believed in, and what she thought was right. Putting Chuck in a hole in the ground was definitely against what she thought was right.

The General watched Sarah through the monitor. The conviction was visibly written all over her face. She had begun to respect Sarah Walker since the 49-B. Although she was against the blindingly obvious rejection of protocol and orders, Walker had done what ultimately had turned out to be in the best interest of not only her, but Bartowski and the nation itself. Ms. Walker had backbone, did what she believed was right and a code which she could respect. The general mused over her thoughts, although she remained expressionless.

Beckman let out an audible sigh which made Sarah jump as the sudden expression of emotion surprised her.

"Walker, what I am about to tell you is above your pay grade and top secret. You are not to inform anyone on what you are about to learn except Colonel Casey and Bartowski." Sarah nodded.

"As you know Chuck downloaded the newest version of the Intersect, 2.0 of his own free will. As this is a joint operation with the CIA I have undergone negotiations with the new director on how we should proceed with the new Intersect.

The NSA wishes to put Chuck into spy training so he can control the latest upgrades to the Intersect efficiently and become a true spy. That being said the Director wishes to put Chuck under 24-hour observation in holding and perform tests to understand the latest changes to Bartowski's brain, which I strongly disagree against." Sarah swore she saw the General shiver at the knowledge of what they would be doing to Chuck.

"We have hit a wall Agent Walker. And it's not looking good. What do you suggest we do?" the General asked. Sarah was surprised to say the least, but quickly regained her composure; she had been given a rare opportunity to have a hand in Chuck's future. She pondered this for a second.

"Well?" Beckman asked.

"Chuck is not cut out to be a regular spy. If he was to become a spy he would lose the parts of his personality that make him so special. He would stop being himself."

"I understand Walker, but you're going to have to give me more than that."

"Although his personality makes it impossible for him to become a regular spy, those same parts of his personality is also what makes him the perfect Intersect."

"... Go on."

"Chuck is kind, caring, and thinks that everyone can be saved. Although that makes him difficult to control during missions, and a stubborn fool-" She smiled slightly when saying this. "It also allows him to use the Intersect to its full potential.

His environment and the way he thinks allow him to do anything, to get out of any situation, to save anyone, no matter the odds. With the new Intersect this is increased even further. If he was to be trained as a spy, to be forced to leave behind his family and friends, his effectiveness would dip well below any other agent in the field right now, and we would lose someone extremely valuable."

"But what should we do if not give him Spy training? The intersect 2.0 was design to be used in a spy, it wasn't designed for someone of Chuck's calibre."

"I have an idea." Casey said as he walked down the stairs into Castle.

"Colonel Casey, what do you have in mind?"

"Chuck isn't regular. He couldn't even be a regular spy even with the Intersect. He doesn't think that way." Casey voiced, he quickly shot Sarah a look,

"So I say we train him different training. We give him different rules. We give him special clearance. We let him call the shots. After watching his quick thinking and strategic skill at the incident with the Ring without the Intersect, I think it would get the most out of him and the team."

"I see Colonel Casey. I agree, Chuck has never been one for the regular rules, and his courageous act stopped the Ring gaining control of the Intersect and still gave us the advantage against his best interests. He may indeed deserve that. However there is one issue. There are reliability issues that I can't ignore." General Beckman stared at Sarah for a long moment.

"We all know," she said. "That you have been more effective at getting productivity out of the Intersect because of his feelings for you."

Sarah was a little puzzled at the tone in Beckman's voice. "Yes, ma'am," she said cautiously. "It has also caused some problems. It frustrates him that I can't reciprocate."

"I can see where that might be frustrating," Beckman agreed. "For both of you. It's a shame that some silly rules might be keeping us from doing what's right."

"Yes, ma'am," Sarah said.

"On the other hand," Beckman said. "If the team continued to be effective, rules would be very hard to enforce. Don't you agree? We'd be forced to depend on you in the field to make sure the right thing was done."

Sarah grinned as she understood the General's meaning. "Yes, ma'am," she said.

"You two have provided an excellent point; and I will take this information into my deepest consideration. However, I cannot promise anything." Sarah felt the weight lift of her shoulders.

"I will be staying in contact with you and Colonel Casey and brief you as the situation unfolds. If this works out we will discuss the details of how this will affect the team. Chuck is not to be moved from his current position under any circumstances and removed from duty until further notice. You two are to protect and guard him for this period. For now ignore any and all communications from the CIA."

"Thank you General." She was blown away.

"Oh and Sarah, I am on your side on this, so try not to go and pull another 49-B. You're dismissed." Although her tone was deadly serious, there was a hint of a small joke. Before Sarah could reply the link had been cut.

Sarah was stunned. She had just gone from having to commit treason, again, to keep Chuck safe, to having the NSA on her side. 'Maybe Chuck has grown on the General as well' she thought. Sarah turned to Casey.

"Thanks for that Casey." She smiled at him; he just gave out a huff.

"Don't worry about. It's the least I could do. He's given up a lot for this country. And he's done it out of he's own head, no one asked him to do it. He's either an idiot or a real patriot. And we all know how much of a smart ass he is." He said with a grin.

"But why did you say you want Chuck to call the shots?" Sarah asked.

"I saw the way he was one step ahead of everyone at that building. And it got me thinking. Over the past 2 years, why was it that his ideas were the only ones when the shit didn't hit the fan? He's got brains. I wouldn't mind taking orders from him if he didn't rub it in my face, would you?"

-

Chuck was in the kitchen making pancakes and whistling to himself. He felt the best in 2 years. Not only had his pain disappeared for some miraculous reason but instead of having the Intersect hanging over his head, the thought that he had done this out of his own free will calmed him. He heard a knock at the door and put down the pan before strolling over to the door. When he opened it he was surprised to see Casey and Sarah standing at his door.

"Hey guys, what's up?" he said with a grin.

"We just saved your ass Bartowski." Casey smiled as he barged in. He quickly sniffed the air, "Mmm, pancakes."

"Can we come in Chuck?" Sarah asked, Chuck could tell by the sparkle in her eye that she had good news, it made his heart soar.

"Sure, but i think Casey beat you too it." He joked before stepping aside to let Sarah in, "So what did you mean when you said you saved my ass?" he quizzed.

"Walker here got orders to bring you into CIA custody behind the NSA's back and put you in a hole. She told Beckman. She's breaking orders for you dumbass. Got any syrup?" Casey voiced from the kitchen.

"Sarah, Is that true?" he asked, shocked.

"I couldn't stand by while they put you underground Chuck. I couldn't let that happen."

"Hey idiot. Where's the syrup?" Casey growled.

"Top cupboard." Chuck shouted back. "Ok guys. One thing at a time, tell me this from the beginning, what the hell is going on?"

"Maybe we should sit down." Sarah suggested as she pointed to the table. Casey just huffed in agreement. Chuck sat down at the head of the table as Sarah and Casey sat either side of him, Casey holding a plate of pancakes smothered in syrup.

"Ok guys, from the beginning." Chuck said. Casey had his face stuffed with pancakes so it gave Sarah the chance to explain.

Chuck just sat there and took in everything Sarah said, and the few snarky comments Casey would put in every now and then.

"So you don't think i can be a spy?" Chuck asked, obviously hurt. But before Sarah could console him Casey jumped in.

"That's right dorkus. You're not cut out to be a regular spy, you care too much. You'd have to kill people, to follow orders no matter how shady, to care about no one except yourself. Do you really think you could do that?" Casey asked. Chuck went to retort, but couldn't think of anything to say, Casey was right, he cared too much. Chuck's face dropped and Sarah sent Casey an icy glare telling him he'd gone too far.

"Hey, what are you moping about? I said regular spy. That doesn't mean that you're going to have to go back to the buy more and be a lab rat for the government. We're going to do this our way, after all since when did you ever agree with the regular rules?" Casey said with a grin.

"What do you mean?" Chuck asked, lightening up a bit.

"He means Bartowski, that you're being given a special opportunity that no one else has ever gotten." Beckman's voice rang out throughout the room. All three turned to the Flat screen TV mounted in the Lounge room.

"General Beckman. That was quick." Sarah said surprised.

"This was a very important situation that required immediate action. Mr. Bartowski, have Agent Walker and Colonel Casey briefed you on the situation?" she asked as the three walked to in front of the monitor.

"I think for the most part General." Chuck replied, "We got to where Casey joined the conversation."

"I see. Well for this conversation I think that is enough. I think Agent Walker should brief you with the rest in private." Chuck looked at Sarah confused; she had a faint blush cross her cheeks.

"So Mr. Bartowski, do you agree with Casey and Walker's opinion on your training?" he looked at Casey and then Sarah. He held her gaze for a second before turning back to the monitor.

"Yes i do General. I trust they have made the right decision."

"Good, than that will make this a lot easier. I have informed the president of these latest circumstances involving Agent Walker and the Director. Needless to say the Director has been discharged and until a new one can be found the CIA is currently under the jurisdiction of the NSA. After taking into consideration your suggestions and the familiarity you two have with Mr Bartowski and his methods and reviewing the records of the missions I have decided that it would indeed be the best course of action. Effective immediately both Agent Walker and Colonel Casey are to create a training regime specially suited to Bartowski's needs and submit it to me directly for analysis. If I find it to be acceptable you will begin training. Once your training is complete we will discuss how to move from there. Any questions?"

A unanimous "No ma'am" sounded out.

"Good. Dismissed."

Casey shuffled on the spot for a moment until he realized that no one was moving. Then it hit him. Sarah was waiting for him to leave. "Well I'm going to go back to my place," he said. "I'll see you later Walker to get that stuff sorted."

Once the door had shut Sarah turned to face Chuck. "Chuck, I have something to tell you." she said, nervousness written all over her face.

"You were going to stay weren't you?" he said softly looking at the floor.

"How did you..." she said surprised.

"Bryce told me, before he died." He said sombrely before looking up at her, "Is it true?" he asked, as if the answer could crush him.

"Yes, it is Chuck. When I was standing there at Ellie's wedding, I realised that this was where I belonged. I had real family, real friends. It wasn't a cover anymore." Chuck took a step towards her, closing the gap to inches.

"But Sarah, what about your job? The CIA?" He said, almost whispering. Her proximity was sending his senses into overdrive. Her smell, her presence. It was sending him crazy.

"The job was my life. But then i met you. You changed everything Chuck." She whispered softly. He looked into her blue orbs, and could see everything. The many emotions that shone though her eyes. And that's when he saw Love. Love so deep it scared her. Love for him. His body moved of its own will. He slowly tilted down and closed his eyes.

Her mind was a mess, she couldn't think. Everything about him was moving though her, overwhelming her. She couldn't stop her body even if she wanted to, she was too far gone. Every part of her screamed this was right. She leaned up slowly, closing her eyes.

Their lips met softly, sending sparks coursing through their bodies. He slowly wrapped his arms around her waist, gently pulling her flush with him as she wrapped her arms around his neck. They broke for air before quickly smashing their lips together. Where the last kiss was innocent, this was passionate. His hands began to roam her back as she intertwined her fingers with his dark brown hair. There kissing became urgent and fervent and they began to make their way down the hall.

They quickly crashed through the door and dropped onto Chuck's bed. Chuck's hands began to move Sarah's shirt up as she arched her back. He soon began to place soft kisses down her jaw line and down to her collarbone. He slowly trailed down until he was at the lace of her bra.

"Chuck, please." Sarah breathed. It was all he needed to hear before his hands moved to the clasp of her bra.

-

A/N: Aww just when it was getting to the good bit too :P Sorry people but I suck at Lemons, like really bad. That's why this first chapter stops here. If someone wants to take over and write the lemony scene for kicks, that's fine by me, do I get to beta it??

Hope you all enjoy, please Review and leave your thoughts, every little thought counts, it helps me and the story get better ^_^

The Next Chapter: Sarah and Chuck finally confront there feelings after last night, and the training begins!