A/N: So here it is my first ever attempt at a fan fic, be gentle with me. This is mainly AU and I got my inspiration from the interview between Larkin and Flemming in Vs the Alma Marta, specifically the line "he's in, no matter what." It got me thinking, what would happen if Chuck had been asked to join the CIA and Stanford and he had said no. What would be the fall out from that decision.

Disclaimer: Don't own Chuck

Chuck vs. the consequences of saying no.

Stanford 2003

Chuck sat in the hard chair outside of Professor Flemings' office wondering why he had called to see him. He knew that he was doing well in his class, in all of his classes, but other than his college work couldn't think of any reason why they would need to speak. He had been sat waiting restlessly for a quarter of an hour when the Professor finally opened his door and asked him to come inside.

"Chuck, I'd like to talk to you about your test results from last week" Fleming opened "they were very, very impressive. 98%. No one else has even come close to that score before".

Chuck blushed and muttered something about studying hard and guesswork.

"I forwarded your score to some people I do recruiting work for, and they would like to make you a job offer".

"Wow Professor, who is it? Is it Roark Industries?"

"No, and this will not leave this office under any circumstances, it's the CIA". Chuck looked at Fleming, his mouth slightly ajar. Of all the scenarios which had gone through his head whilst he was waiting to be seen, this one hadn't featured in the slightest.

"The CIA…" he managed to stutter out, "Why on earth would they be interested in me?"

Fleming looked sternly over his glasses at Chuck "They see great potential in you and believe that you have a skill set which could best be utilised by them in the service of your country"

"Do they want me to do computer work for them? Coding?"

"No Chuck, not that, they would like you to become an agent."

Chucks mind had gone into overdrive, images of James Bond and Jason Bourne flashing through his head, glamorous, dangerous images. He didn't say anything for a minute trying to take it all in. He surprised himself by the questions which came out when he finally did manage to speak. "What about my sister? Would I be able to tell her? Would this endanger her in any way?" That wasn't what he thought he would say at all.

"Chuck, you wouldn't be permitted to tell her anything, in fact you would be encouraged to have as little contact with your family and friends as possible. It's a profession with inherent risks and keeping your distance from them would help to keep them safe".

Chucks face dropped. "Professor, do you know anything about my family history?" Fleming shook his head. "My Mother walked out on us when I was 9, and my Father left when I was 15 and we have heard nothing from either of them since they day they left us. My Sister brought me up, without her I would have ended up in care. She sacrificed so much for me; I can not abandon her and do to her what our parents did to us. I refuse to"

"The opportunity to serve your country should be considered a great honour"

"I know it is, I understand that sir, I really do, and if I could explain to her what I was doing perhaps my answer would be different, but I can't do that to Ellie, I can't make her think that I would be willing to leave her too!"

"I really think you should think very carefully about your response"

"It wouldn't change anything, I can't hurt Ellie like that"

Their discussion went in circles after that, neither party willing, or able, to change their position. Professor Fleming was forced to dismiss Chuck without receiving the response he had been hoping to get, he then made a phone call to report what had happened, one he had been hoping not to make.

"Sir, this is Fleming"

"No Sir, he refused"

"Yes, I recorded the conversation as instructed; I will email it to you immediately"

"I did ensure that Mr Bartowski signed a non disclosure agreement to cover this interview"

"What would you like me to do next?"

"Yes Sir, I will leave this matter in your hands, and not mention it to him again"

Two months later

It was nearly midnight on a Friday evening when Chuck left the library; he had been finishing off a paper for one of his professors which would hopefully gain him more credit towards his degree. Chuck had tried, and largely succeeded in putting his strange interview with Fleming to the back of his mind, but it had taken some time and much conscious effort on his part to achieve this. It had however had the net result of firmly focussing him on what he wanted for his future. At the start of his final year at Stanford he had been planning to work hard and play hard to make the most of his remaining time there, this had changed following his interview. He now wanted to complete his degree as quickly as possible so that he could get a job and start helping Ellie out financially whilst she completed her training to become a Doctor. He wanted to start paying her back for all she had done for him and this was one way in which he felt that he could help. He had even begun to send his résumé out to potential employers, but so far had heard nothing back, which concerned him a little but it was still early days.

He turned his phone back on as he left the building and started to walk back along the quiet road to the room he shared with Bryce. He had the place to himself as Bryce was away, again, for the weekend. His girlfriend, Jill, was also away visiting her family in LA. He had to admit to himself that his relationship with both Jill and Bryce had suffered over the last two months as he was putting all his energies into studying and spending very little time on socialising. Although he had some twinges of guilt about neglecting them, he hoped that they understood why he was working so hard. When he checked his phone he found he had a missed call, it was a message from Jill. He happily went to listen to it, looking forward to hearing her voice. What he heard stopped him in his tracks.

"Chuck, I'm sorry" she said, "but I think we should break up. It's not you, it's me. I need to concentrate on my studies and what I want to do next, and I just don't have time for a relationship. Please don't call me or try and see me. I'm so sorry"

Even though he knew they had spent little time together recently, Chuck hadn't been expecting this. He was shocked, stunned and desperately wanted to talk to someone, but didn't know who to turn to. Normally he would speak to Bryce, but he was away, and Chuck knew from experience that he never answered his phone when he was on his weekend trips. Morgan would still be up, and happy to talk, but Morgan had never tried to hide his dislike of Jill and he really didn't think that he could get impartial advice from him, in fact Morgan would probably want to take him out to celebrate. Ellie was the perfect person to speak to, but given the time, and her busy schedule he knew that he couldn't speak to her until the morning, which is what he reluctantly decided to do. What really worried him was that he had no idea whether to be upset or relieved that Jill had taken this step.

Walking distractedly, his mind churning over what had just happened, he failed to notice the black van which pulled up in front of him until its doors burst open and two masked men jumped out. Initially Chuck didn't panic, he thought that it was a couple of his Frat buddies pulling a prank on him, however that assessment quickly changed. These men knew what they were doing, their movements concise and efficient as they grabbed him and bundled him into the back of the van before he had any chance to raise the alarm. Despite his struggles and protests he was soon immobilised. Chuck felt a sharp prick in his arm, even as he looked down and saw the syringe things started to turn black and he rapidly knew no more. The van sped off, taking its hapless passenger with it.

Unknown time later…

On awakening Chuck found himself on a bed in a sparsely furnished room, his head was thumping and his mouth dry, he felt disoriented, alone and scared. On a desk across from the bed were a couple of bottles of water and some aspirin, he got off the bed, staggered across the room and gratefully downed them.

"Don't freak out, don't freak out, don't freak out" he repeated as a mantra to himself as he looked around the small room. Apart from the bed and the desk there was a chair and a small chest of drawers, but no other furniture or decoration. He looked down at himself and realised that he was just wearing his t-shirt and boxers, the rest of his clothing, shoes, phone, and bag had vanished, this just added to his feelings of vulnerability and unease. The room had two doors and a small, high window, with no visible opening. The first door he opened lead to a small bathroom, the second door was very firmly locked. No amount of effort could shift the door and no one responded to his shouts of protest. He started examining the room thoroughly, and aside from a few basic toiletries in the bathroom, there was nothing to be found, there was certainly no evidence of his missing clothing or belongings. Given his height he was able to look out of the window, but the angle was poor and his main view was of a grey, wintery looking sky, which told him that he probably wasn't in California anymore.

There was no real way of telling how much time had passed, bar the gradual darkening of the sky through the window. He was sitting on the edge of the bed, having worried himself to a state of near exhaustion when he finally heard the door being unlocked. Through it walked a large, imposing looking gentleman, Chuck could clearly see three other people through the open door, although they remained outside as the door closed again. Chuck didn't say a word, he really didn't know where to start, he just looked at the other man and hoped for an explanation which would make some sense of what was happening to him. He tried to keep the very real fear he was feeling from showing, but his eyes gave him away.

"Mr Bartowski, my name is Langston Graham and I am here to speak with you about the offer we made you two months ago". For a split second Chuck looked at him blankly, then, with a feeling of increasing sickness his mind jumped back to the interview he had had with Professor Fleming. He didn't realise it, but he was unconsciously shaking his head, trying to deny his worst suspicions.

"But I turned that down" he said weakly, desperately trying to get this thoughts into some semblance of order. "I didn't discuss it with anyone, honestly. I promise! Why would you do this, take me like that? Why would you kidnap me, I'm nothing special"

"Oh you're special" Graham said with a humourless smile "Your test results at Stanford proved that. You should have accepted our offer, this could have been much easier on you but you left us with no choice. You should consider yourself drafted as you really have no say in the matter now, not that you ever did"

"But why?" Chuck asked again "Do you do this to everyone who says no? Where am I? What is going to happen to me? What have you told my Sister? Please." He didn't like how defeated that final please sounded, but he couldn't hide it from his voice.

"You're at one of our training facilities and you have absolutely no need to know where that is. Tomorrow morning you will start to learn the skills you will require to perform the role you have been selected for. I expect you to put as much effort and dedication into this as you did for your Stanford studies and will accept nothing less. The penalty for failure, at any stage, will be severe. Your Sister, does not know where you are, or what you are doing, no one who knows you does. If you hit the training targets set for you I will permit you to make one brief phone call to her, to let her know you are okay, nothing more. This will be very closely monitored and if you abuse this privilege, fall behind in your training targets, disobey the orders given to you by your Instructors or try to leave this establishment it will be discontinued and no future contact with your Sister will be permitted. Do you understand what I have told you?"

"You're not giving me a choice" It wasn't a question.

"No, we're not".

Graham got up to leave the room, pausing as he was about to open the door "I understand that your Sister is very important to you, remember that by working for us you will be helping to protect her and her way of life. Do it for her. Here is your first test, you will undertake your training under an assumed identity, this will help to protect your family and friends. By tomorrow morning I expect you to be fully conversant with your new cover". He opened the door and one of the waiting men passed him an A4 brown envelope, which he left on the desk for Chuck to read. "Welcome to the CIA Mr Bartwoski" he said as he left, the door locking behind him.