A/N This is my first attempt at a multi-chapter fic. The story is my attempt to deal with the aftermath of Chuck downloading the 2.0. I will try to keep the story driven by the characters and not force them into reactions and situations to fit a faulty, poorly thought out story idea. I hope this will be true to Chuck, Sarah and Casey or at least as I saw them. I won't promise there will be no angst and as a matter of fact this first chapter already is rather dark but I will promise there will be no contrived relationship geometry but drama? I hope so. It starts the night after Chuck said "Guys, I know Kung Fu" and all canon is respected up till that point. But as canon didn't respect the fans after that point I won't respect it from this point on either. Again I am not a writer, I'm an engineer so please as John Lennon once said "I hope I pass the audition."

I'd like to thank BDaddyDL for looking the original draft over many months ago and helping me learn things about how to do this. I'd also like to thank esardi and Gabriel Fell for giving the latest version a read through before I threw this out to the ether. All ideas and suggestions are welcome. I'd like to get better at this as I have a long way to go. Hey I know there are many season 3 retcon fics out there but I just needed to get some of this stuff off my chest.

BTW I don't own Chuck because if I did the dropped plot device this season would be Morgansect!

Chapter 1.

The Decision

Why did he do it?

Sarah had been asking herself that question ever since she saw him take out those 5 Ring operatives. For the 2 years she had known him all he ever wanted was to get The Intersect out of his head and have his normal life back. In that fact he never wavered. Even when it seemed that his life and his heart were on a never ending roller-coaster ride that was the one constant among a sea of variables.

She looked around the darkened hotel room that had been her "home", well as much of a home as a spy could ever have, these past 2 years. She turned on her side and glanced at the one thing that actually meant something to her in this room full of the color green. There resting on her night stand was a picture, a picture of two people smiling brightly back at her, their picture. To any outside observer it was a picture of two people completely and totally in love. To her employer however it was just a cover. But for her and Chuck it was so much more than that, but they couldn't talk about it openly. Sarah just hoped he knew when he came over and saw it there that she felt it too.

Now as she tried in vain to get some sleep she ran all of the moments from the last 72 hours through her head for what seemed like the millionth time. She thought back to Barstow and a seedy, dingy motel room on the side of a forgotten highway.

Thinking about that morning in Barstow had brought her so much joy and excitement for the first 48 of those hours. But now what it brought her was confusion.

Let's face it Sarah Walker was no prude and certainly not a virgin but that morning was unlike anything she had ever experienced in her life. Even having sex after watching that amazing sunset on the catamaran with Bryce in Cabo those years ago didn't come close. She had thought for so long that that day was as good as it could get for someone like her, someone with a past and someone who could never truly fall in love. Sex with Bryce on the ocean was great but it wasn't making love. It never was with him. It was just one beautiful person enjoying physical contact with another beautiful person. It was fun and she thought it was enough. She even thought at one point that she loved Bryce and in a way she probably did, but they were never IN love. It simply wasn't part of their makeup. They were great spies and great spies don't fall in love. That was rule number 1 and every spy knew it from the very first day at the Farm. But somehow Barstow was different.

Even though they never actually had sex it was unlike anything she had ever known. His touch was electric. The way their hands intertwined was like they were exploring a whole new universe that neither had ever seen before. Well at least not Sarah. He was so gentle and so patient that when they finally let go and kissed each other it was like the dam had finally broken. Her heart just overflowed into the warmest place she had ever imagined. It was like her heart had finally found its home, its other half. The place it truly belonged. When he pulled back and gave her that brilliant Bartowski smile, the one melted her icy walls every time, the one she fantasized about so many times on so many sleepless nights, she felt safer and happier than at any moment in her life. Sarah Walker was in love and she was loved by the most amazing man she had ever known. His kisses, their kisses, were filled with passion, tenderness and something completely unknown to her. This man adored her and she had never felt that from anyone else before.

Sure other men had told her they loved her but it was more they lusted after her and wanted to get into her pants. There were marks she had manipulated to lust after her before she got the intel she needed and then dumped them wanting something they were never going to get. Bryce once said he loved her but it was never real and they both knew it. There was that tall member of the Harvard crew team she met orientation week who took her virginity and then dumped her as fast as the next skull went under the Mass Ave. bridge. He said he loved her but he had probably said that to 10 freshman virgins he met that week alone.

Nothing she had ever known had ever prepared her for that morning in a flea bag, no tell motel on a lonely road outside of Barstow. Chuck had joked that he half expected to see an old woman's body looking out the window of the main house when they pulled in. He was just happy that the manager's name wasn't Norman. Even Sarah Walker got that reference and smiled for the first time that day on the run. Even in the most terrifying of times Chuck always seemed to find the humor in things. He shot her a grin and a wink and she knew he was just trying to lighten the tension in the air as much for himself as for her.

Sarah rolled over again to get away from the annoying clock that seemed to be standing still next to "their picture". She thought back to that morning and the fact that the most amazing intimate moment in her life had just happened and they never even got to second base. "How is that possible?" she asked herself when she was getting ready for the rehearsal dinner. How could something so PG be the most erotic and sensual experience of a world class spies life? It just wasn't supposed to be that way but the more she thought about it, felt the warmth in her heart, the more she knew it was real. That's why when Chuck held her hand and told her it finally felt real, she answered "It is real". Because it WAS real. More real than anything she had ever known. If only Devon hadn't said what he said as they were all enjoying a drink in the bar after the dinner. "Hey, maybe you guys are next?" Everyone laughed and smiled. Chuck had an enormous but nervous grin on his face after he said it until he saw the terror in Sarah's eyes. No one else caught it as she tried to cover it with a smile but Chuck knew better. He knew that this was going way too fast for her so when he suggested that they head home separately she thanked him for understanding even though all she had thought about all evening was getting back to where they left off at the "Bates" motel. But that was so Chuck. He always knew what she needed him to do and it almost always meant sacrificing what he wanted for himself. He was uncanny that way and it was one of the thousands of things she loved about him if she would let her guard down enough to admit the truth that everyone else clearly saw. He was the only person in the world that truly saw and cared for the girl inside the beautiful agent's body.

But then at Castle that next morning after Chuck rejected Beckman's offer and she had given Sarah a new assignment that terror came screaming back. How could she think of a future with Chuck? How could someone as special as he is really be happy with someone who had done so many horrible things in her life? Besides she was afraid she couldn't give him back the kind of love he truly deserves. It just wasn't possible. He had told her months ago that they couldn't have a future together when she was on the verge of telling him she cared about him even more than he did about her. Why hadn't she insisted on speaking first at the fountain? Why had she let him build up her hopes and then send them crashing down to the ground again? If only she had told him how she felt and that she would use those feelings to protect him even more than before. She knew she hesitated taking that shot and it almost cost him his life but she would learn to use those feelings to make her a better protector and more committed to never let anything happen to him. But instead she let Chuck tell her there was no future for them. He simply couldn't accept what they did have as enough. It had always been more than enough for her. As a matter of fact it was everything to her. Their "cover" relationship was the most fulfilling and wonderful part of her life. It was more real to her than anything she had ever known but he could not accept anything less than it being absolutely real. She knew he deserved that and that she couldn't give it him, not then at least. If only she had spoken first she might have been able to ask him to be patient a little longer with her. Maybe she could find a way to get closer to him. Maybe she could tear down that wall and then maybe her real could become his real but she never got that chance. Or more accurately she never asked for it because she wasn't good enough for someone like Chuck Bartowski.

But then a few months later at that same fountain he told her after Cole had left that he was "going to get this thing out of my head one day and when I do I'm going to live the life that I want with the girl that I love. I won't let this thing rob me of that, I won't". She knew deep inside that he was talking about her. He had made that quite clear. She had not reacted with more than a glance because she still didn't think it could ever happen though on the inside she was screaming for it and that girl to be her.

But now after all that, after Barstow, after Orion had removed "that thing" from his brain when he and they finally could have "everything that he has always wanted" why did he decide to put it back in? Why put himself through that? Why throw it away when it was finally within their grasp? All she could think of was that it was her fault. She again had been frightened and rejected him for what may be the final time that ended any possible future. After Chuck had opened his heart to her so selflessly and asked her to "do me the honor of taking a vacation with me" she hit him in his most tender area, a spot that had never fully healed and now certainly never could. She told him she was leaving, and to make it even more excruciating she was leaving with Bryce. It was as if she had taken every knife she had ever thrown in her life and jammed them directly into his heart. The devastated look on his face as he walked away was probably the same one he had when he walked away from the fraternity house at Stanford for the last time those many years ago. He had been betrayed by his best friend again. And he had been rejected by the woman he loved once again as well. What made it worse was that she knew all about it. She knew what this would do to him and yet she did it anyway. How could she be that cruel? How could she destroy such a kind and caring man? How could she hurt the best friend she had ever known? The man that gave her Barstow? That gave her hope that there is something more to life and she has worth so much more than just her body and her job? Chuck Bartowski had been betrayed once again and it happened at his beloved sister's wedding. All because she, kick-ass ninja spy girl was afraid. How pathetic was that?

She sighed for the thousandth time that evening. That had to be the reason he did it, she thought. He was lost, hurt and alone so he grasped for something that made him feel special. Something that made him different. Something that would help everyone else, everyone else but him. The love of his life was leaving and would be gone forever so as he always did he gave up his own desires for everyone elses because she had already taken those away from him. And she did it with Bryce.

Sarah leaned her head back and scrunched her eyes lids closed to hold back the tears that were now forming. If only she had not panicked. If only she had told him how she really felt. How Barstow had changed everything for her. How her life, their life, would never be the same after that morning in the motel. If only Devon wasn't Devon. If only she had finished what she started to say to him on the dance floor. If only, if only, if only. That was the story of their lives. And it seemed like it never would change.

Sarah sat up in her bed and put her head against her knees and the tears began again. Now things could never go back to the way they were. Now they could never have Barstow again. She had pushed him away and back into the spy life and had manipulated him to do something like she had done so many times before. Chuck had wanted to get it out of his head and have a normal life with her. Something that deep inside she desperately wanted as well but her fears coupled with years of training had destroyed that possibility and maybe would lead to his death. The new Intersect would make him an even bigger target for Fulcrum and this new threat, The Ring. Sarah Walker was responsible for putting that target there just as if she had drawn it herself. And maybe, just maybe, she had built his coffin as well.

Why did he do it?

She had to know the reason. She had to tell him she was sorry. She had to get him to run with her. It was the only way. She had been preparing for that possibility ever since that night with Longshore. Ever since she thought Casey had been given the termination order. She knew that ultimately there were only 2 choices for Chuck as long as he had The Intersect. Bunker or death. And now that Orion had finally given him a third option, she snatched it away from him because she was scared. She was terrified of normal and she took away his normal future, their normal future.

She whispered to herself. 'I have to make this right. I have to get him to understand why I said what I said. Why I was wrong, why I was afraid. I have to get him to forgive me. I have to tell him the truth, I owe him that much.' He deserved to know that especially since that life was now gone forever. Then she had to do her job. She had to protect him. They had to run. It was the only way she knew.

Sarah looked back at the clock. It said 3:10 am. She hadn't slept a wink all night. She had run through this scenario countless different ways and she always came to the same conclusion. She was the reason Chuck downloaded the 2.0. Hell she may have even been the reason that Bryce was killed after she told him she wasn't coming with him. Maybe if she had been there none of this would have happened. Maybe she would have been able to have saved Bryce, protect her former partner. Maybe Chuck would never have been there in the first place. Then she could have found him and told him she had changed her mind and wanted desperately to go on that vacation. After all she had started to tell him that when they were dancing in the courtyard at the reception. She told him "I don't want to save the world, I want…..." And because of her he was there trying to be the hero once again. Trying to help his nemesis, the man that was taking away the woman he loved all over again and he knew that because of what she had told him before the wedding. "The mission is classified but I'm working on the new Intersect Project… with Bryce" Kryptonite could not have hurt him anymore than Sarah Walker did

Yet there he was, no Intersect, no training, and no backup against well trained Fulcrum agents or so he thought. Agents that had just mortally wounded the cause of so much of the pain in his life. The man he lost the only two women he had ever loved to. He was coming in second to that guy all over again. But all he could think of was trying to help him. Trying to save another human being, a friend. Trying to just do what was right no matter what it cost him. One more time, Chuck was that guy. Even after the spy life had destroyed his sister's first wedding he took what they had given him as compensation for all his pain and commitment to his country and gave his family and the other most important person in his life the wedding she always wanted. He had already done one of the most thoughtful things Sarah had ever seen but here he was again putting himself in danger to protect the man that destroyed his life not once but twice and doing it just because he was Chuck after all. Chuck was the hero and what did he get for it? Blindsided by the emotionally crippled woman he loved. Or so she thought.

Sarah took a deep breath. She had to fix this. She had to know why he did it. Why did he make that decision? What could she do to make it up to him? Each time she came to the same conclusion. They had to run and they had to run now.

When they had told Beckman what had happened she was stunned to say the least. She mobilized a new protection team. Chuck wasn't safe and she didn't know if the world was safe from Chuck. She at least had to have him under 24 hour armed protection until they knew more about The Ring. What did they know about the Intersect project? How deep were they infiltrated into the intelligence community? How large were they and how big of a threat? But the bigger question was, did they know about Bartowski? Did they suspect he was the new Intersect 2.0? What skills did he now possess and could he control them? Could he be trained? Could he now be the agent they had always envisioned the human Intersect to be? At the very least they needed time to answer those questions before they made any final decisions about whether to train him, bunker him, or ultimately kill him.

Sarah knew that the new protection team would be arriving at Castle at 9 am and she was ordered to have Chuck there when they arrived. Casey would be watching him in Echo Park overnight so if they were going to run, they had to do it before then. She had to go get him now and not look back. It was his only real hope and yes it was her only hope as well. She owed him that. In fact she wanted that. Being on the run with Chuck was far better than living with the guilt of crushing him and then seeing him change into a completely different person. A person that the CIA had always wanted him to be, a cold heartless super agent. Bryce Larkin and John Casey rolled into one tall, handsome, nerdy frame. General Beckman's wild card enforcer with a skill set 10 times what she had when she fit that role for Graham. She couldn't stand the thought of seeing someone so kind, so unique, so loving turned into well,,,,, her. Or at least what she was before she walked into the Buy More 2 years ago and he started a change in her that was still going on to this moment.

With that Sarah jumped out of bed, quickly got dressed, and grabbed the bag she had packed just before Graham had been killed by the Fulcrum cipher. A bag that had new passports, cash and enough clothing and ammunition to last until they could leave the country on the first part of the plan she had drawn up. They would head to Canada and grab the next set of stuff she had stashed in a storage facility outside of Edmonton. She knew Mexico was closer but everyone expected them to go south, so she would go north. Besides dressing for the cold Canadian plains would help hide their identity a lot easier than the 100 degree heat in Panama.

Sarah was a planner. She always had been. She planned many of the cons with her dad even as a child. She was smart, organized and clear headed. She would need all of that if she was going to keep the man she loved, the man she had betrayed by her own insecurities safe from well, everyone. Now she had so little time to execute the plan she had started a year ago in case they ever tried to bunker him again.

She looked at the clock again, 3:20 am. She would only have a 5 hour head start before the team would arrive at Castle. That wasn't anywhere near what she wanted but it would have to do. She needed to go get Chuck now. Just as she was about to grab the bag, her keys and her Smith and Wesson she heard a gentle knock at door. She panicked. Who could be here at twenty minutes after 3 in the morning? It could only be bad news. So she took the safety off on her sidearm and slowly crept towards the door and the peep hole when she heard another knock. This time it was slightly louder and then just as she was about to aim her gun, open the door and put three rounds center mass into whomever was knocking at her door so late she heard a voice. She heard her favorite voice in the world call her name quietly so not to wake anyone else up nearby.

"Sarah?"… "Sarah, are you awake? It's me. Sarah, I'm sorry, we need to talk!"

A/N 2 Hey I know this was mainly narrative but the next chapter will be a lot of dialog. I'm going to try and stay one chapter ahead and post a new chapter when the next chapter is basically completed. Hopefully I can keep that pace. Chapter 2 is mostly done and 3 is outlined. 4 and 5 are at least in the idea stage. So any suggestions would be welcome. Any interest in this story? Feedback is definitely appreciated.