A/N - I do not own Chuck although if I did, Sarah and Chuck would have had a condom during Chuck vs the Colonel and they would start S3 as a married couple (those who read The End Is Only The Beginning can attest to that:D).

Anyhoo, since I am addicted to writing fanfic currently, I was toying with different ideas and the one to really stick out was the fact that I think fate plays a big part in Chuck's life although his choices are purely driven by the type of person he is and who he would like to be. This just explores an alternate timeline where Chuck's a professor at Stanford, Sarah's still a CIA agent and Bryce is the Intersect. Would their choices change, would they really end up in a different place? Maybe the destination is the same but trust me, the journey will be so different :).

Just wanted to thank wepdiggy for reading the first draft and giving me the idea for the flashbacks. I pay homage to the King of AUs :)

The Inevitable Life of Chuck Bartowski

Chapter 1 Pieces of a Puzzle

Silverlake, Los Angeles, 8.00 pm, 18th September 2007

"Chuck, I'm not going to fight with you on your birthday. We'll talk about it later." Ellie let's out another exasperated sigh as she notes the hurt expression on her brother's face. She really does love him but at times like these, she has to remind herself that she's the older one and that it's her job to look out for him when he's too blind and pig-headed to look out for himself.

"I don't want to fight either but it's our dad. How can you.."He lets his sentence trail off as he runs his fingers though his hair. He knows he needs a haircut but between his research at the University as well as his after hours search for his father, he really does not have any spare time. The only reason he drove out to LA was to tell Ellie the possible good news. She was the one who had taken the initiative to throw him a surprise party. "Ellie, I think I found him." Chuck does not want to sound too hopeful because it's not the first lead he has had although it does seem to be the most promising.

"No" She does not like sounding shrill or being the one to cause his face to fall but it seems that it's all she's been doing for the past few years ever since he took it upon himself to search for their dad. "Don't you understand, he left us and he didn't come for our graduations or called on our birthdays. He's gone and I say good riddance." Ellie blinks away the tears, not wanting to rehash the past and relive the hurts.

"How can you say that? Maybe...maybe he had a good reason." He sees her shut her eyes, her hands clenched by her side and he knows that he has gone too far. "It's ok, we'll talk about it later. Awesome said you invited real doctors for my party, you know cause my doctorate doesn't rate." He smiles and holds out his hand, hoping that she accepts the truce he's offering. Chuck knows how much Ellie had to give up in when their dad left. She had worked all through medical school and still ensured that he finished college and graduate school as well. She never complained but he understood that the abandonment had hurt her irreparably and it was the one thing she had asked him not to pursue.

"I....I can't do this anymore. I can't see you try and find him and each time you fail, I have to pick up the pieces. All the while dreading the fact that one day you might succeed." Her voice is thick with emotion, her tears spilling over because she can't hold back any longer but still she tries to swipe them away.

"What are you saying? Ellie?" She's been all he's had for so long, that it's inconceivable to contemplate not having her in his life. "You can't mean it?" The incredulity is evident in his voice as he holds on to her arms and forces her to look at him. It's then that he sees the truth reflected in her eyes, that he's been hurting her with his quest but that he's also powerless to stop it.

"I'll be here when you stop looking." She does not want to do this, does not want to give him an ultimatum but as his big sister, she knows she has to do something. He's practically put his life on hold, just concentrating on his research and in his spare time, looking for their father, wanting answers he does not need. She wants more for him but realizes that he has to want that for himself as well.

"I...I'll say goodbye to Awesome" He leans in and kisses her on the forehead, closing his eyes to her tears as he turns away. He cannot explain the gnawing need he feels that compels him in his search for his father but he also cannot continue to hurt his sister. It's not a choice he wants to make but understands that perhaps it the only choice available for right now. Chuck does not look back as he walks away.

Stanford Quad, 11.21 am, 23rd March 2009

"Professor Bartowski!"

Chuck looks up from his prone position in the middle of the quad and has to shield his eyes to see who has called out his name. The sun's out and it's the first taste of sunlight he's had in weeks so he really does not feel like entertaining any of the student body currently. However, he's still just an Associate Professor with no tenure and if he does not publish soon, the dean's probably going to ask him to leave. The only thing going for him was the fact that he kept getting the highest attendance in most of his classes and all the students voted him Best Lecturer three years running. He can see Alice, Fleming's Teaching Assistant waving at him from the side and he does not have the heart to ignore her so he waves her over. She's a pretty brunette, slim and tall although Chuck has always been reminded of Ellie each time he sees her.

"Hey Alice, what can I do for you?" Chuck can't figure out why she blushes so much when he talks to her and he's always been too polite to ask.

"Umm, hi umm, Professor Fleming sent me to ask you umm if you umm, can take his classes for the next two weeks. He says he has a breakthrough in his program and needs time to umm, refine his paper." She tries not to look into his brown eyes because the last time she did that, she lost her train of thought and just stared for a good minute before he asked her if she was having a seizure of some sort. Unlike the other girls on campus, she didn't speculate as to why he did not date rampantly through the female population on or off campus. The current betting pool had gay and secretly married tied at two to one odds. Alice just knew that both were way off the mark and that the truth was more mundane. She saw his worried looks every time Professor Fleming talked about one of his published papers and knew that all Professor Bartowski wanted was to finish his own program and publish it to gain tenure. That's why he didn't date despite having most of the graduate students and some of the other teachers drop hints the size of anvils about their availability and dearth of weekend activities.

Chuck knows he cannot afford to anger George Fleming who by all intents and purposes has been his mentor these past few years. Even more than that, he's probably been his only friend and confidant besides Morgan. He wished it was different and that people like Jill and Ellie were still in his life but he can't regret the past any more than he can change it despite wishing otherwise. "All of them?" He's pretty sure that George knows that he still has his own program to finish and that the dean has given him an ultimatum. However, he's also quite sure that George is still too self-centered to care. Chuck knows he can say no but friendship and loyalty prompts him to refrain from refusing.

Alice just nods, not really liking the task at hand. She knows that he's been working nights and weekends and has had to take over Fleming's class a number of times this past year. She wished he would say no and to stand up to Professor Fleming but she can see that he's a soft touch and feels even more compelled to help him knowing that Fleming's doing more than just taking advantage of his good nature. "I'll help, if..umm..I mean if you need help, I'll help. Grade papers, set the umm, tutorial schedules, anything you need." Alice can't help the blush that reddens her cheeks as he smiles widely at her. She does not deserve the smile and it adds to her guilt.

"That's really nice of you but wouldn't professor Fleming want you to help him with his project and also have time for your own work?" Chuck could definitely use the help but he knows what's its like to be a TA and the workload they carry. He has never liked taking advantage of people and would not like to start now.

"Umm, no, he said that I can assist you if you do take his classes." Actually Professor Fleming's exact words were to do anything to get Professor Bartowski to say yes, so she does not feel like she's being desperate for volunteering her time. She hopes eventually that he'll finish his program and when he does, she'll be there waiting for him.

"Ok, thanks. Well, I'll see you next week in class then." Chuck smiles and stands up, dusting himself off. If he's going to take extra classes next week, he cannot afford to spend anymore time out here, soaking up the sun, and knows he needs to get back to his office and continue working on his paper. Chuck doesn't often regret his life choices but on days like these, it's difficult to accept that all he really has is his half finish program on three-dimensional textured subliminal imagery and nothing much else, no private life and not much of a family. Eventually he hopes that tenure and perhaps finally calling Ellie and maybe even saying yes to one of the offers of a date would finally fill the void he often feels. He looks wistfully at the laughing students surrounding him as he makes his way back to his office, head down, hands in his pockets. He does not see the same wistful look on Alice's face as she looks at his retreating back.

Marriabbad, Pakistan, 2.13am, January 13th 2008

Sarah's running along the streets, trying to stay in the shadows and back lanes. The bottles of morphine and antibiotics clanking together in her coat pocket. She wanted to burn the hard drugs she saw in the room but could only handle one mission at a time. She'll try her best to go back later in the day as soon as she finishes what she needs to do. She can't afford to let the medicine bottles break so she slows down finally stopping in a small back lane. She removes the morphine and places it in her back pocket. The headlights of the car illuminate her suddenly as it turns into the lane and she does not have time to do more than roll away as it barrels towards her.

The three men that exit the vehicle are already surrounding her, one pulls off her hood and her long blond hair tumbles out catching them by surprise. It's enough of a distraction for her to kick back and catch the nearest one in the throat. She sees the gun in the holster on the one to her left and she immediately tackles him to the ground, his elbow catching her in the chin. Sarah smashes down on his solar plexus, stunning him and removes his gun just in time to shoot the third and hit the second one across the jaw with his own gun. The sound of the shot echoing off the walls of the buildings surrounding them. She did not want this to happen but does not have a choice now as she runs towards the main street once again. It's only the sound of a thud that stops her in her tracks. The three men are still prone on the ground and but she checks them nonetheless. It's only when she hears the sound of something being hit does she note that it's coming from the trunk of their car.

Sarah knows she cannot afford to waste too much time but she also believes that the enemies of her enemies may become her ally. She slowly makes her way to the car and pops the trunk, the gun in her hand held firm as the trunk opens wide.

"Don't you touch me" The voice is belligerent and most definitely female.

"Carina?" Sarah can see that she's hurt, a gash across her scalp bleeding sluggishly while the bruises are forming on her arms and face. She helps her out of the car and can see the recognition on her face.

"Sarah? What are you doing here? Where's that bastard Bryce." She's unsteady on her feet but the fury she feels is enough push her forward as she grabs for Sarah's arm.

"That's not fair and you know it. Bryce didn't give the order, just the intel." Sarah does not like the defensive tone her voice has taken on but she knows that it's becoming more and more the norm. Explaining away the small inconsistencies in the information or even covering up the blackouts were now part of her job." How did you end up in the car?" This mission had been a bust from the start. The DEA never played nice with anyone and only wanted the use of the Intersect ignoring the fact that both her and Bryce were top-notch agents.

"Martinez approved the raid but there were too many of them and there was a firefight, I got ambushed and stuffed in the trunk." Carina can sense that there is more to Sarah's story, "Why were they pursuing you?"

"Bryce is hurt and they had a full medical store so I thought that they would not miss any. I guess I was wrong." Sarah hopes that Carina is too angry and too full of righteous indignation to probe any further. Bryce had flashed as soon as he had entered the building, passing on all the information to Martinez. They had then been sent back to the campsite with the lone prisoner caught at the site. It was only in the car that the prisoner had started talking and triggered another more intense Flash which gave vague directions to their main warehouse where all the drugs were being kept. Bryce had called up Martinez and had been relaying the information when the nosebleed started. He had passed out soon after which prompted Sarah's own raid on the warehouse.

"Martinez won't let this go." Carina, moves unsteadily towards the car and buckles herself into the driver's seat. She does not want to have to choose sides and therefore does not offer Sarah a lift as she starts the car.

"Bryce did his job and Martinez will have to go through me and Graham first." Sarah knows that it's partially an empty threat but one that Carina will take back. She does not look back as she turns and runs back towards the campsite, hoping that Bryce would at least have regained consciousness by now.

CIA Headquarters, Langley Virginia, 8.53am, 23rd March 2009

Bryce's head feels like its about to explode and the four advils he has taken has done little to ease the pain. He's in one of his bespoke suits although the collar seems too tight and he feels so constricted, like his skin is pulled too taut around his body. He knows Sarah is surreptitiously glancing his way, unsure of what to say but wanting to give him some sort of support so she just settles for putting her hand on top of his. He concentrates on the soft weight of her hand, feeling the warmth it provides while regretting that it's all the physical comfort she'll ever give him. Luckily, the nosebleeds have not started as yet although if he takes into account the extent of the pain currently, he knows that it's only a matter of time.

He wills the door to open and to let them into Graham's inner sanctum. He wants to get this review over with so that he can finally take stronger medication and knock himself out until he's needed again. It's not the life he envisioned for himself but Bryce knows that he does make a difference albeit a small one, in the fight against Fulcrum. He hears a belligerent voice in the hallway and closes his eyes, not wanting to see the person it belongs to. He feels Sarah's hand press down slightly harder on his and is grateful for her non-verbal gesture. He knows how much it is costing her to support him here but the sad truth is that she is all he really has.

Major John Casey strides into the alcove, back ramrod straight, perpetual scowl on his face, which transforms into a snarl as he notices the two sitting agents. He closes the phone he had been shouting into and goes to stand next to the window. He has to control his temper, knowing that he's in CIA headquarters and not back at his own stomping grounds. It is a difficult task to wait in the same room as the man responsible for killing his partner. He catches Agent Walker's eye and is taken aback at the defiance he sees there. Surprisingly, it does not increase the anger he feels but gives him pause. He knows her background, decorated agent with more than eight years experience in the field. She had been the one who had risked her life and stayed with Pete as he lay bleeding on the ground. She was the one who had torn up her shirt and tried to stem the blood flow to no avail.

It's only then that the door finally opens and the three people are ushered into Langston Graham's office.

"Sit down" Graham does not bark out the words but both Agent's Larkin and Walker can recognize an order when they hear it and they take two of the chairs that have been arranged in front of his large oak desk. It's just now down to a contest of wills between Casey and Graham as they stare down each other. It's only when the large screen on the wall, comes to life and General Beckman comes online, does Casey relent and take the remaining seat.

Graham sighs as he prepares to start, not liking what he has to do but understanding that inter agency policy dictates that it is necessary currently. A life had been lost, not senselessly per se but still, there was a good possibility that it could have been avoided. "I call to session this informal review on the 23rd of March, year 2009, in order to fully understand the steps taken by Agent's Larkin and Walker that could have led to the death of one Captain Peter O' Shea two days ago in a compound in Odessa, Texas."

The headache has now reached its apex and Bryce has trouble following every word that Graham has spoken. He can barely sit upright but forces himself to do so, knowing that both their careers depend on it. He looks over at Sarah and can see that she knows the strain he's under by the sad smile that graces her face. It does not completely soothe the immense pain in his head but it does give him a small measure of comfort, as does her voice when she speaks for the first time.

Sarah can see that Bryce is on the brink of one of his bad spells. There's no medical term for it although she knows Dr Busgang has referred to it as an unfortunate side effect of Bryce's brain trying to adapt to its unusual usage as the Intersect. To Bryce, it just meant uncontrollable pain and to her it meant that she needed to be more vigilant and protective of him during the time that the pain would incapacitate him. She realizes she needs to move this review along because by her count, Bryce has less than an hour.

"Sir, if I may?" She let's the question hang there, knowing that Graham just wants this over, with as little damage to the CIA's reputation as possible. Because of it, Sarah knows that she has to protect Bryce at all cost and not let them hang him out to dry. What happened was a tragedy but it still did not mean that Bryce did not do the best job he could. The damn Intersect in his head had malfunctioned again providing them with incomplete data. It was a replay of Pakistan but this time, Pete had not been as lucky as Carina. Having said that, it was still the NSA's decision to move in despite being told that they were not a hundred per cent sure of the validity of the information. "As you know, Agent Larkin and I have been seconded to Major Casey's team for the past three months. Our main task was to infiltrate a white supremacist organization with links to Fulcrum. Agent Larkin's additional mission was to gather information that would trigger Intersect Flashes and allow us a greater understanding of Fulcrum's US operations."

Bryce clenches his jaw, the room is beginning to feel warm but he knows he cannot show any weakness now. It's takes a huge effort to speak but he does so anyway, knowing that Graham expects it and Casey doesn't. "The first few Flashes were good." Casey's interjecting grunt does not phase him as he continues," giving us intel on their other bases. Unfortunately, the longer I was there, it seemed the information from the Flashes I received became less and less reliable. The last one was three days ago regarding a potential bioweapon shipment to the Odessa base from an external unknown seller." He slowly stands and makes his way over to the small fridge in the corner where he helps himself to some water. The walk taking a lot out of him and its only by sheer will is he still standing. It's the first time he has looked directly at Sarah and he can see the worried expression she has been trying to hide, her eyes full of concern. He leans back against the side cupboard, his arms folded, his eyes now looking into the distance as he recalls the next part.

"I informed Major Casey and Captain O' Shea of the shipment but also the fact that we were not sure of it's reliability." Bryce had come back from a run and in passing one of the brotherhood, had overhead a code word that triggered a Flash. He had barely made it into their room before collapsing and having a seizure, which wiped out most of the information provided by the Flash.

Sarah knows that she should tell Graham the truth about Bryce's deteriorating condition but now is not the time. All she can remember right now is the feel of Pete's warm blood on her hands as she frantically tried to stem its flow only to realize that it was useless. She has to remind herself to not look at her hands and instead concentrate on Bryce's voice." Captain O'Shea still felt though that the information was enough to trigger a response team to intercept the shipment." She had liked Pete. Had liked him enough to actually say yes when he had asked her out on a date four months ago. He had taken her to an Irish pub and they had drunk Guinness and eaten meat pies and she would have liked to be asked out again, only Pete had died in her arms two days ago.

"Is that right, Major Casey?" General Beckman has never been a proponent of the Intersect project although its earlier successes did somewhat ameliorate her strong negative views. However, the string of recent failures has shown that it is definitely time to upgrade the project and take it out from the CIA's sole aegis. Dr Busgang was working on too old technology with no access to anything new. The work with Bryce Larkin seemed to have hit a brick wall some time ago and even now, she can see that he has not been faring well. The new Intel she has received on Roark Industries Intersect cube may be just the solution she needs. If all goes well, it'll be the last intel she'll have to share with Graham before usurping the whole project for the NSA.

Casey nods, "Yes, ma'am. Captain O'Shea intercepted the delivery truck and we decided that he would perform the exchange. We were working off the premise that this was an unknown faction doing the sale as per the intel from Larkin." He cannot help the venom in his voice as he spits out Bryce's name. That was the crux of the matter. Although Walker kept insisting that the information was too vague, it was Larkin who had insisted that it was a new source, which they needed to shut down. He can see that the man can barely stand currently but cannot in any way drum up sympathy. Larkin had volunteered for the Intersect project and for the first few years, had lorded his superiority over the other agents. It's current malfunctioning state served him right although it did put the people around him at risk, like Pete and especially Walker. "That intel proved wrong and the moment they saw Captain O'Shea, they opened fire."

Sarah remembered hearing the gunshots and running towards the truck. She heard Bryce calling her name but she couldn't stop her forward momentum. She recalls the next part in great detail although her voice does not betray any emotion. "Pete had been wearing a vest but the Brotherhood had been prepared and had armor piercing bullets. I managed to get him out of the truck while Agent Larkin provided cover fire. I…" She had blown their cover, only realizing it when Bryce had to draw fire away from her and towards himself. "I broke cover and tried to save Captain O'Shea but his wounds were too extensive." She can still feel the blood pumping over her hands and has to again consciously stop herself from looking down at her fingers.

Bryce had been so sure that the information he retained from the Flash was correct, that he was still contributing to the fight against Fulcrum. "I'm sorry." He knows that the apology cannot bring back the dead or reclaim back months of undercover work but it's all he can say right now. Busgang had told him that without a better Intersect upgrade, he only has a few months left in the field anyway. He's banking on Fleming to come up with the break though he's been secretly working on. Bryce knows that Fleming's been blacklisted due to his suspected dealings with a few shady foreign organizations but nothing could or had been proven. Besides, in the most recent message from Fleming, he had talked about a breakthrough in the data architecture he was using. Bryce hasn't even told Sarah about any of it, not because he doesn't trust her but because he's afraid she'll lose more faith in him. All he needs is some more time. "Captain O'Shea's death was a tragedy but Fulcrum is still winning this war and right now, the only source of information we have is right here." Bryce taps the side of his head.

"I'd rather fight blind than have unreliable intel. We should retire the Intersect project before any more people have to die unnecessarily" He glances at Walker as he states this and although she does not react to his statement, he can see her hands curled into fists and knows that he has made his point. Casey knows it's not going to be his choice anyway and that Beckman's probably not going to shut down the project anymore than Graham is. He can see it in their demeanor. Pete's death was just an unfortunate blip in the way they viewed things, they were bureaucrats sitting in their offices, giving orders but never fully realizing the human consequences.

"While I agree that that particular intel was bad, I see no reason to scupper the entire project. The time and money invested coupled with the possibility of an upgrade does not justify shutting it down." Graham does not need to look at the screen to know that the General has also agreed with him. They had talked earlier and this meeting had been just a formality to appease Major Casey. Bryce was definitely damaged goods but he is still their best Intelligence link in the fight against Fulcrum and other enemies of the US. Both Walker and Bryce still had the highest success rate out of all current CIA officers even despite this most recent setback.

"Then I think I am done here." Casey does not slam the door on his way out although he's more than tempted to do so. He barely glances at Larkin but can see that the man is close to collapsing, probably still standing due to sheer will and the fact that he does not want to cause his partner anymore trouble.

"The both of you will take the requisite psych evals over the next few days and report back for your next assignment. General Beckman has fresh information on a new Intersect cube that we need to retrieve." Graham does not acknowledge the look that passes between Walker and Larkin. He's almost sure that they do not have a physical relationship going on but he can see that they're as close as partners can get.

Bryce does not say anything as he walks out of Graham's office, knowing that Sarah is following closely behind. At least he makes it to the stairwell door before collapsing against it. It's Sarah who rushes forward, her body pushing the door fully open as Bryce falls headfirst. She catches him before his head hits the ground. She slowly slings his arm around her shoulder and makes her way down the three flights of stairs all the while supporting his weight as best she can. She slowly guides him to the small infirmary on the second floor where she waits, holding his limp hand, until he recovers. This is not the first time this has happened and Sarah is already familiar with the symptoms as she takes out his handkerchief to stop the nosebleed that has already started. She's not sure how long he has and prays that perhaps this new Intersect cube will be what Bryce needs to get better.

The End

So, I am really interested in your opinion and views of the premise and the story. Anyway, to help, the poll for this chapter is A) Please continue because it's interesting, B)No, not that interesting so think of another story, C) I would just like to review because (add own comment)...:-)