A/N Hello again, I thought I would start this new story since Bryce vs Everybody went over so well… lol. This story starts at the end of Season 2 episode 20 Chuck vs The First Kill and it's a "what if" story, what if Sarah didn't run with Chuck. Oh, I have not stopped Bryce, as I told several of you in PM's it is going to be a slow story. Anyway I hope you enjoy this one, it is a little dark, but dark with a light.

I do not own Chuck.

Chapter 1 - Smiling Faces Sometimes

The mood in Castle was bleak, to say the least, of all the missions they had run in the past year, none had been such a resounding failure. On top of not saving Orion, they had let Jill Roberts escape. Agent John Casey and Agent Sarah Walker were supposed to be the best, yes they have had failures before, but none to this magnitude, and now here they sat at the briefing table in Castle, with General Diane Beckman staring down at them from the large monitor. Although the pause in her rant had only been seconds it had seemed like hours. Enough time for both of the agents to examine every line and wrinkle on her face, enough time to watch her face turn red with anger and when she did finally speak again the sound of her voice made both of the agents wince. "How could you let Jill Roberts get away?"

"I'm sorry, General… I took her inside the building because I didn't have a choice." Sarah Walker said in a determined voice.

"So, not only do we have no idea where Steve Bartowski is, we have a Fulcrum agent who knows all of our secrets running free. Where is Chuck now?"

"He's on his way to the Buy More," Sarah informed.

"Permission to drop the twerp into a deep dark hole, General," Casey said, knowing that it wouldn't happen but showing his annoyance of the whole situation.

"Granted…" and with that one word from the General, everything changed. "It's over… the Human Intersect project has become too hard to control. I can't afford to wonder anymore if this team or Chuck Bartowski is a liability."

Sarah had stood and walked quickly to be right in front of the monitor and said: "What are you saying General?"

"I'm shutting down this project. Chuck's going into lockdown. He'll be taken to Washington and put into a secure facility once and for all."

"Operation Moron is over?" Casey whispered more to himself than anyone else listening.

"You're making a mistake, General," Sarah said

"I have made my decision, Agent Walker."

"Chuck isn't going to go down without a fight," Sarah said in an attempt to sway the general.

"That's why there won't be one."

"What do you mean?"

"Chuck trusts you, Sarah. He believes you would never betray him. Use that. Go to Chuck. Tell him we intercepted his father while being transported and he's back at Castle. Agent Casey will be waiting here. He will tranq Chuck. Then, he will wait for the extraction team to arrive for his transfer. That is all." The screen then went blank and the NSA seal appeared.

Casey gave Sarah a small sad smile and walked over and pulled out the case with the tranq gun in it. "How can you just stand there and say nothing?" the anger evident in Sarah's voice

"Beckman's right. The safest place for Chuck is underground. What do you think is going to happen when Fulcrum finds Jill, anyway?

Sarah slowly walked across the parking lot to the Buy More; her emotions were all over the place. She doesn't want to put Chuck in lockdown; she wanted him right where he was, with her. But she knew she could not disobey a direct order, she was a good agent and she followed the orders of her superiors. If she did not do this it would be a dereliction of duty, she could and most likely would be brought up on charges. Her heart sank to her stomach when she walked into the Buy More, and she saw Chuck walking right toward her. It was time again to be an agent.

"We have good news," Sarah said to Chuck, forcing a smile to her face.

"Can it wait? Computer emergency" he said shaking the keys to the hearder.

"It's about your father. We found him."

Chuck looked at her with a questioning look and said "What? How? Where is he?"

"One of our recon teams intercepted his transport as Fulcrum was moving him. He's back at Castle. He's safe, Chuck. It's all over." Sarah finished with a big smile on her face.

Chuck released a big breath and sighed and smiled a full smile at Sarah. "I owe you and apology."

"Why?"

"I was beginning to think that I couldn't trust you anymore, Sarah. That maybe Jill was right, that the CIA was never going to let me go, that they would always put their best interest ahead of mine. But not you. You've always looked out for me. Thank you." The whole time Chuck was speaking, Sarah could feel her smile failing her, she felt that now she was betraying the best man she had ever known, a man that she lov… cared about very much. What can she do, her mind had begun to race, she had to figure out a way to make things right, and then, in a split second, she knew what she had to do. She leaned in to hug him and just as she was going to whisper in his ear to remove his watch, just as she was going to tell him his father was still out there, just as she was going to tell him "we have to run" she saw them. Three men wearing dark colored suits and wearing sunglasses, three men that she recognized from the Fulcrum headquarters that they had just left, three men that were now running towards them.

"Come on Chuck we got to get out of here."

"What… What's going on, Sarah? Where're we going?" Sarah didn't answer but pulled Chuck through the parking lot toward her car. Then she saw two more men standing near her Porsch, so she pulled him into the Orange Orange and down into Castle. Just as she was going to tell Casey that they were being followed by Fulcrum agents, she heard the all familiar "whoosh" of the tranq pistol. Chuck reached up and pulled the dart out of his neck and looked at Sarah. She could see the hurt in his eyes, she could see the sadness, and she could see her betrayal. Chuck willed himself not to pass out, and turned to Casey and said: "Save my father."

Casey said: "You have my word," and then shot three more darts into Chuck's chest. As Chuck started to fall, Sarah rushed over to catch him and then eased him down to the floor; she looked at Casey and cried "What have you done?"

"My job."

####

He could hear a voice, but it sounded like it was at the other end of a long tunnel. It was a female, but he didn't recognize her. He decided not to open his eyes, and just listen; he needed to find out where he was, and what had happened to him.

"How long has he been out?" Chuck heard a man's voice ask.

"Almost 48 hours," the woman answered, "how many tranq darts did they use?"

"According to the report, they used 4 darts," the man said with a chuckle.

"Is this funny to you Sgt.? They could have killed him using that many. Who are the idiots that did this?"

"Major that would be, Colonel John Casey of the NSA and Special Agent Sarah Walker of the CIA." Chuck's heart sank, he already knew, but to hear it out loud, to hear he had been betrayed by the two people he trusted most to protect him was almost too much for him to take. And on top of that, they both got a promotion for their "great deed". Chuck could not help himself and let out a sarcastic snort when he thought of the promotions. The Major heard the snort and walked closer to Chuck's bed and looked at him, while she was checking over Chuck, she continued her conversation with the sergeant.

"Do you watch wrestling, Sergeant?"

"Umm… sometimes ma'am" the sergeant answered wondering where this was going.

"My little brother used to love the WWE, and there was a wrestler called The Big Show, you know him?"

"Yes, ma'am, he was billed as the world's largest wrestler."

"Yes, that is him," the Major then turned and faced the sergeant and yelled "YOU WOULD NOT EVEN USE FOUR TRANQ DARTS ON HIM! I want someone held accountable for this. You will write up a recommendation for punishment on these two agents."

"But ma'am these…"

"What?!"

"Nothing ma'am I will take care of it." The Major then walked over to Chuck's bed and saw a very small smile on his face.

"Well looks like someone is playing possum," the Major said as she leaned in closer to check Chuck's breathing. "You can open your eyes now, Mr. Bartowski". Chuck opened his eyes slowly to let them adjust to the bright fluorescent lights above his head. His mouth was very dry and he was still dizzy, but he was awake. "My name is Major Andrea Chang, I am a doctor with the NSA and I will be taking care of you until the tranquilizers wear off." Chuck's eyes were able to focus and he looked at the woman that had been talking to him. Major Chang was dressed in her neatly pressed Air Force uniform; she was an Asian American that if Chuck had to guess was about 5' 6" tall. She had jet black hair that she wore in a bun and had soft brown eyes.

"Where am I?" Chuck asked with a scratchy voice.

"You are in Washington D.C., Mr. Bartowski."

"Chuck…"

"Excuse me?"

"Call me Chuck…"

"Ok… Chuck, you are here so I can make sure you are healthy enough for the next part of you journey."

"Which is?"

"I'm sorry, I am not privy to that information, but the General will be here soon."

"Oh great…" Chuck said letting out a sigh.

####

Chuck had been moved to a room, a room with no television, no phone, and no windows. This must be what my life will be like now, he thought, four walls, a small table, and a bed. Chuck's depression was pulling him deeper and deeper, it had been 5 days since he had been taken and the only person he had seen was Major Chang, but she didn't have any information for him, or she wouldn't tell him if she did. Chuck was lying in his bed with his eyes shut when he heard the door open, figuring it was the major he didn't open his eyes and just waited for her to start.

"Mr. Bartowski…" he knew that voice, it was the bane of his existence, General Beckman. Chuck just laid there and did not acknowledge her at all.

"Mr. Bartowski, I am talking to you," the general was getting a little agitated; she was not used to being ignored.

"What did you tell my sister?" Chuck said softly not opening his eyes.

"Mr. Bartowski, we will get to all of that but first…"

"What did you tell my sister?!"

"Mr. Bar…

"WHAT DID YOU TELL MY SISTER!"

####

Sarah stood in Casey's old apartment. Most of the surveillance equipment had been removed, but a few cameras were still in place. Sarah stood motionless as she watched two California Highway Patrol officers walk up to Ellie and Devon's apartment. She watched as they knocked on the door and she watched Ellie open it. She watched as the officers spoke. She watched as Ellie fell to her knees screaming and crying uncontrollably. She watched as Devon ran to her, fall to the floor and took her into his arms as he cried. Sarah then straightened her posture, turned off the monitor, walked to the bathroom and vomited.

####

The general sighed in defeat, she knew she had to answer this question or she would never get anything out of him. "Your sister and friends were told that you and Sarah were involved in a traffic accident. Both Sarah Walker and Charles Bartowski are now dead. Chuck let out a primordial scream that shook the room and caused the general to take a step back. The doors burst open and Major Chang ran in and grabbed Chuck by the shoulders and tried to calm him. She cut her eyes to the general and said in a harsh tone, "What did you do?"

"Watch your tone Major!" The general had to get back in control of this situation.

"On this side of the building I am in charge General, now what did you do?"

"I told him the story that we told his sister to cover him being gone."

"Well, that was stupid…"

"MAJOR!"

"Sorry, ma'am," Andrea said with all the sarcasm and bile she could put into her voice. "I am going to need you to leave until I can calm him" The general turn on her heels and headed out the door, once out the door she leaned hard against the wall and put her head in her hands, this was not going well at all.

"Chuck… Chuck… I need you to calm down," Andrea was trying her best to calm him without medication, but she was failing horribly, finally and with great apprehension she ordered a sedative. She had just gotten all that crap that the NSA pumped into him out and now she had to add more, she was not happy. Chuck felt the needle and then he felt the effects, his breathing became easier and his mind became quiet, he looked at Andrea and mouthed "thank you," as he fell into a deep sleep.

The next morning when Chuck woke up he wasn't in his tiny little room; he was in a large bed in a very large apartment. Chuck eased himself up and began to look around. The bedroom was big, bigger than his old bedroom and this one had a king size bed. Chuck found that a little ironic, but he moved out to the living area. There he found a large television with a DVD player with hundreds of DVDs. He also noticed that they had gotten all the game systems and games anyone could want. On the bookshelves, he saw books, graphic novels, and comic books. It looked like someone had held up a comic book store. He then went to the kitchen and found it stocked with snacks and soft drinks. By the phone was a menu for the cafeteria, he picked up the phone and it started ringing without even entering a number. "Kitchen" came a voice from the other end and he just hung up. Over on the desk was a computer and a stack of files with a note on them.

Mr. Bartowski,

Read over these files, if you flash on anything, e-mail the information to me. My e-mail address is already on your computer.

General Beckman,

And so it begins, Chuck thought to himself, as he opened the first file.

####

General Beckman had told her assistant that she did not want to be bothered, and usually when she said that she would go all day without any interruptions. But today was different, not 30 minutes after she walked into her office, the intercom was sounding. "General, I hate to bother you, but a Major Chang is here and she says it is urgent."

The general let out a big sigh, she knew that the Major was in charge of Bartowski's wellbeing, and knew whatever the Major had to say, she did not want to hear. "Send her in" was all she said.

"General, we have a problem," Andrea said without any hesitation.

"What's wrong now, the wrong kind of comic books?" The general was tired of all the concessions she had to make just to keep Bartowski happy, and she really didn't want to hear anything today. He had been on lockdown for three months now and it seemed like every day it was something.

Andrea just shook her head at the general's lack of interest in Chuck, but continued on, "No ma'am, but if we don't do something fast he is going to die."

"WHAT? What do you mean? Is he sick?" the general was now starting to show some interest.

"Ma'am, for the past 2 weeks all he has done is his work on the files and sleep. He has almost stopped eating. He has stopped watching movies and playing his games. When we let him outside he walks to the middle of the yard and sits facing west. He has lost almost 20 pounds in the last three weeks, if he keeps this up, he will shut down soon."

"Can we force him to eat?"

Andrea shook her head again in disbelief "No ma'am not unless we put a feeding tube in him. But I do have an idea."

"What's your idea, Major?"

"The Island, we have total control of it, he could come and go from his apartment, he wouldn't be a prisoner. "

"Major, you know as well as I do the Island is for rehabbing agents, not for locking down assets."

"That is why it is perfect, people will think he is an agent, and he will be surrounded by agents to protect him. All I know is he cannot go on the way he is."

The general did like the idea of Bartowski being far away from her, then she would not have to put up with all his inane request, and even if she didn't show it she did want him to be healthy.

"Okay, we will send him to the Island, but I am not just going to let him run loose, I will read in an agent that is there and they will become his protection detail."

"That's a good idea," Andrea said thoughtfully, "just make sure they do not treat him like a prisoner. It will be good for him to have some social interaction; I have been told he has even stopped talking to his guards."

"Okay, Major, you make the arrangements and I will go talk to Mr. Bartowski."

"You're going to talk to him?"

"Yes, it is time I set things straight."

####

Chuck was lying in his bed just staring at the ceiling, he was doing what they want, so Ellie and his friends would be safe, but he was not going to do anything else. He was tired of being treated like a criminal. What had he done that was so wrong? Why is he being punished, all he did was everything that they asked of him. For the tenth time that day and the one millionth time since he had been locked up, he cursed Bryce Larkin, and just like every time he thought of Bryce, he thought of her. He had thought he could trust her, hell he thought she may have even loved him, but here he was all locked up proving once again what a gullible nerd he was. In his whole life, there has only been one woman that had not disappointed him and she thinks he is dead now. He let out a small moan as he thought of Ellie and the more he thought about Ellie and the more he thought of "her" the more depressed he got. Something had to give soon; he just couldn't take it anymore. Chuck had flopped over on his stomach and buried his face in his pillow when the doorbell to his apartment rang. He slowly extracted himself from the bed and moved toward the door. Then he yelled, "you have the key come in." To say he was surprised to see the general would be an understatement, he had not seen her since he forced her to tell the cover story of his disappearance.

"What can I do for you General, am I not getting the reports done fast enough for you." The tone of his voice was strained and weak; Beckman could see he was having trouble standing.

"I hear you are not eating, Mr. Bartowski. I am hearing all you do is sleep and work on the files."

"I thought you would be happy, you have everything you ever wanted. A subservient intersect, at your service ma'am. Isn't that why you locked me up, so I have to do everything you say? All I wanted to do was save my father… Did Casey find him?"

The general looked at Chuck, contemplating telling him, but she decided to tell him the truth and said: "Yes, Major Casey rescued your father." She decided not to tell him that Fulcrum had been defeated, no sense in giving him false hope of every going home.

"Major? I thought he had been promoted to Colonel."

"Well he had, but when the report came in on how many tranq darts he used on you, he was busted back down to Major."

"So my father is okay and he is with Ellie, okay I can live with that."

"Yes he is doing well and your sister was married on schedule."

Chuck smiled at the thought that Ellie was able to go ahead with her wedding, he knew she needed it. He was also happy that his father there for her now.

I have some other news, Mr. Bartowski, we are going to move you…"

"To Burbank?"

"No, you know we can't do that, but we are moving you to the Island…" Chuck began to flash and when it was over he looked at her curiously, "You're sending me to a rehab clinic?"

"Well that is its main purpose, but you can live there with no locks, come and go as you please from you apartment and swim in the ocean, interact with the others there, all I ask is you don't tell them about your… gift and start eating and continue your work."

Chuck just stared at her, and wondered what was she up to? But he was too weak to argue, so he just resigned to his fate and said: "Anything is better than here, so when do I leave?"

"Is tomorrow soon enough?"

"Perfect"

Next: The Island

A/N All reviews are welcome, as long as they are constructive. Don't just say "That's sucks," say something like "That sucks because yadda yadda yadda" If you don't want to leave a public review PM me or call me at … nope!