I do not own Chuck. There. That's out of the way.

This is a sequel to my previous fic, 'Chuck versus a Normal Life.' Thank you to all those who read and reviewed the previous story and encouraged me to write the sequel I mentioned in my notes at the end. For all of you, here it is:

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CHUCK VERSUS THE DECISION

Chapter 1

The Sleeper Awakens

Chuck clawed his way slowly awake, as if fighting his way through a layer of gauze. As he neared consciousness, he became aware of another presence, a certain pressure resolving into the feeling of a head resting on his left arm. As his cognizance grew, he began to feel soft hair draped over his arm, tickling his skin. It felt nice. 'I wonder who that is?' he thought. 'Who is in my room?'

At the feeling of Chuck stirring, Sarah woke up. As a trained agent, she had the ability to come instantly awake if necessary. She sat up, stretched, and reached over to caress Chuck's shoulder. "Good morning, sleepy head," she said softly.

Chuck blinked, yawned, and turned to look at Sarah. His throat was still raspy from the breathing tube and lack of use. "Sarah?" he asked. "What are you doing here?" He blinked some more and then looked around. "Where am I?"

Sarah frowned. "You're in the hospital Chuck, don't you remember?"

"I… No. What… What am I doing here?" he asked.

"You were hurt," Sarah said. "Shot. And then you fell and hit your head. Don't you remember?"

Chuck creased his eyebrows and tried to concentrate. "Shot? No. I… I was shot?"

"Yes, Chuck," Sarah said. "This is very important. If anyone asks, you need to say that we were robbed and you saved me from a mugger. You can't tell anyone we were on a mission."

"Mugger?" Chuck asked. "Mission? We were on a mission?"

"Yes," Sarah said. "Don't you remember?"

Chuck looked confused. "No. I… No. How did I get shot?"

'You were a brave, selfless hero who did what no one has ever done for me before,' Sarah thought. 'You threw yourself in front of a bullet to save my life.' But she couldn't tell him that. The agent in her was still too strong. "You did a very foolish thing, Chuck," she said softly. "The North Korean agent shot at me and you jumped in front of the bullet. You're the Intersect; I'm your handler. It's my job to protect you, not the other way around." She knew she should be sterner with him. The Intersect couldn't go around sacrificing himself for a mere agent. He needed to understand that. But the words came out hollowly, as if she was reciting from the CIA Asset/Handler Handbook. She knew she had to make him understand that what he did was wrong, but it was hard to be harsh with the man who had been willing to sacrifice himself to save her life. Maybe Casey should be the one to broach this topic. He could do a much better job. In fact, he would probably enjoy explaining it all to Chuck in excruciating detail. Okay, maybe that could wait until Chuck was feeling better.

"I… I don't remember," Chuck said.

"That's normal," Sarah said. She had dealt with enough injured agents to know a little something about post-traumatic amnesia. Some people never remembered the events leading up to their injuries. "You can tell people that. That you don't remember what happened. What's the last thing you do remember?"

Chuck closed his eyes and furrowed his brow, as if in deep concentration. "I… It's all kind of fuzzy. I remember being at work. And then Casey… No. Maybe it was you… The Castle…" He let out a breath and shook his head, then rubbed his forehead. "I… I can't."

Sarah patted his arm. "It's okay. Don't try to remember. It'll be okay."

"Where's Ellie?" Chuck asked. "When can I see her? I can't believe she hasn't come to see me."

"Chuck, Ellie has been here every day. You saw her, and Devon, and Morgan, and Anna last night. They were all here."

"They were here?" Chuck asked. "I…" He stopped and furrowed his brow. "I'm thirsty," he finally said.

Sarah reached over to the tray and got the cup with the straw and held it up so he could take a drink. "Here you go," she said.

Chuck took a drink, then licked his parched lips and took another. He nodded and Sarah took the cup away. "How long have you been here?" he asked.

Every day Chuck had been in his coma, Sarah had been by his side, only leaving when Casey or Ellie forced her to go home, or more often, to Ellie and Devon's to eat and freshen up. But now that Chuck was awake, the distance between Asset and Handler was beginning to reassert itself. It was automatic, ingrained in her after the almost two years of Operation Bartowski. "Casey or I have watched you the whole time you were unconscious," Sarah said, avoiding a direct answer. "We have your room and the corridor monitored."

"Uh huh," Chuck said. Was that disappointment Sarah noted in his voice, or was she simply projecting what she wanted to hear?

"All your friends stopped by almost every day," she said, changing the subject. "And you've received a lot of cards and flowers, see?" She pointed to the ledge in front of the window of his room which was covered with cards and flowers, many of which were starting to droop a little after being there so long. "And Morgan said he was going to bring your X-Box by today now that you're awake so you have something to do."

"Great," Chuck said, half-heartedly. "That's great."

"How are you feeling?" Sarah asked.

"My shoulder itches," Chuck said, reaching up to scratch only to encounter a large bandage covering his shoulder.

"That's where you were shot," Sarah said. "Itching is good. It means it's healing." She didn't know if that was true, but she remembered her father telling her that.

"I have a bit of a headache," he said. "And I'm kind of tired."

"We have an appointment with Doctor Parker today, now that you're awake," Sarah said. "She's the neurologist assigned to your case. She's the best there is. The CIA arranged for her to come in to monitor your case."

"Well," Chuck said. "That was nice of them."

"Don't worry," Sarah said. "General Beckman arranged for everything. The CIA will take good care of you, Chuck." She stifled a frown. That was a lie, and she was not sure why she didn't tell Chuck the truth. Actually, General Beckman had been willing to terminate Operation Bartowski, assign a low-level agent to monitor Chuck remotely, and write Chuck off. Sarah (and, surprisingly, Casey) had badgered General Beckman to get Chuck the best care possible. It had finally been Casey's argument that Chuck was, in effect, a soldier and the nation had a solemn responsibility to its soldiers injured in the line of duty that had carried the day. That and the fact that two major operations had gone sour since Chuck's 'accident' without the Intersect there to provide the timely intel necessary to successfully complete the mission.

"The CIA," Chuck said. "Well, I guess that's good. I'm not sure my Buy More health insurance covers getting shot by enemy agents."

"Mugged," Sarah reminded him.

"Whatever," Chuck said, a little irritated.

The door to the room opened and Ellie and Devon came in, dressed in their scrubs. "Good morning, Sleepyhead," Ellie said, hurrying over to the bed to give Chuck a hug. "You had us pretty worried, you know."

"We're glad you're back, bro," Devon said, slapping Chuck on the shoulder – fortunately the non-injured shoulder.

Sarah stood up and stepped back so as not to get in the way of the Bartowski family reunion. As she watched Ellie and Devon fawn over Chuck, she felt a little stab of jealousy. As long as Chuck had been in his coma, he had been all hers, or so it seemed. Yes, Ellie, Devon, Morgan and the rest had stopped by to check on him and even to spend a little time, but it had been tacitly acknowledged that Sarah was nurse, guardian and protector. Now, she realized, she would go back to being just the cover girlfriend and everyone else would once again claim a piece of him. She felt guilty for feeling that way, and that simply made her feel worse. After all, she already felt guilty for Chuck being injured in the first place. She had failed in her job. She had failed to protect her asset. More importantly, she had failed to protect Chuck.

"You know," she heard Ellie say, "Sarah has been here every day. All day. We had to practically drag her out of your room to take a little break. I even had them bring up a cot because she insisted on sleeping here with you."

"Oh really?" Chuck said and glanced over at Sarah, a smile slowly spreading across his face.

Sarah felt herself flush and knew she was blushing. Blushing! She was an agent! She didn't blush. "I… It was the least I could do for the man who saved my life," she finally managed to stammer.

"Protecting your woman, Chuck," Devon said. "That's awesome."

"No, it was foolish, "Ellie said. "I can't believe you did that, Chuck. It was a very brave thing to do, but you should have simply let him have the money."

Sarah took a step forward. Chuck was a hero. In fact, he was a hero dozens of times over that no one could know about and no one was going to take away the one time they could proclaim Chuck a hero to the world. "I told you before, Ellie," Sarah said. "It was my fault. I didn't want to give him my purse. If it wasn't for Chuck, he would have shot me. Chuck really is a hero."

Ellie smiled. "Okay," she relented. She gave Chuck another hug. "My brave brother."

"I… I really don't remember," Chuck admitted.

"That's normal," Ellie said. "It's called post-traumatic amnesia. You may never remember what happened that day."

"He also doesn't remember you stopping by last night," Sarah interjected.

Ellie looked at her and then frowned and looked back at Chuck. "You don't remember Devon, Morgan, Anna and I being here last night?" she asked.

"No," Chuck admitted.

"Well, that's normal," Devon said thoughtfully. "Nothing to worry about. After you've had a head injury, sometimes your memory is a little spotty. I'm sure Doctor Parker will talk to you about all of that this afternoon."

"I have a bit of a headache, too," Chuck said. "Can you have them give me something?"

"I'll talk to the nurses about getting you a little something," Ellie said.

"Um, that may not be such a good idea, Babe," Devon said. "I think we should wait and let Doctor Parker prescribe anything. After all, he's her patient."

Ellie gave Devon an irritated look, but then shrugged and her expression softened. "You're right, Devon." She turned and looked at Chuck. "I'd be upset if another doctor prescribed something for one of my patients, even if they were family. I'll give Andi – Doctor Parker – a call and see what you can have. Other than that, how are you feeling?"

Chuck sighed. "Tired," he said. "Even though I slept all night. At least I think I did. And a little edgy."

"Well, make sure you tell Doctor Parker all of that when you see her this afternoon. I'm not sure how we managed to get her on your case, but she's the best neurologist in LA." Chuck avoided looking over at Sarah and smiled. After the little revelation about her staying in his room while he was unconscious, he was beginning to suspect that she had a little something to do with the CIA's 'taking care of him' as well.

The door opened and Morgan came in, loaded down like a pack mule. "Hey, buddy," he said. "Now that you're back among the living, I brought you a few things to pass the time." He began cataloguing his inventory as he dropped things on the end of the bed. "We've got your X-Box. I'm not sure if we can run the Wi-Fi here so you can do online play but Anna said she's check that out. We've got a portable DVD player and the complete series of Babylon Five. I know you were saying you didn't have time to watch it and now you've got the opportunity. I've got the PSP. Some munchies. Oh, and Jeff threw in some DVD's he burned. You may want to really burn those yourself. I'm not sure what's on them." Now unloaded he looked at Chuck and smiled. "Looking a little pasty, there, but it's good to see those baby browns. How are you feeling?"

The infectiousness that was Morgan spread throughout the room and they all smiled. Devon looked down at his watch. "Sorry, Chuck, I've got a procedure in ten. I'll check on you later, bro, okay?"

"Sure, Devon," Chuck said. "Thanks for stopping by."

Since Chuck didn't remember the visit from last night, they spent the next hour and a half regaling him with stories about what had been happening, especially at the Buy More, while he had been out. Sarah sat back and watched from the other side of the room, feeling at once both part of and apart from Chuck and his extended family. Finally, Chuck started to yawn and Ellie suggested they all leave and let Chuck rest. Sarah wanted to protest and stay, but Ellie shooed her out into the hallway.

"You know," Ellie said once they were outside Chuck's room. "I don't think I've told you before, but I am so grateful for all that you've done for Chuck."

Sarah simply shrugged. "I really didn't do anything," she said. "I just sat with him."

"I know that means a lot to him," Ellie said. "And to me, too. I don't know a lot of girlfriends who would have stayed like that."

"He saved my life," Sarah said. "It was the very least I could do. And…" 'And I love him and I can't imagine not being with him,' she wanted to add, but the 'Agent' part of her wouldn't let her admit that out loud, even now. "And he's a very, very special man."

"That he is," Ellie said. "And it's still going to be difficult for awhile. In some ways, his recovery is going to be even harder than when he was in a coma. I just want you to be prepared for that."

"I'm not going anywhere," Sarah said, and she hoped it was true. Unfortunately, she suspected it might not be. When the CIA had tried to reassign her while Chuck was in a coma, she had balked and taken an 'indefinite leave of absence.' She knew they only granted it because, first, it was standard procedure to allow some downtime for an agent who had lost her asset so she could 'get her head back in the game' and, second, they weren't concerned with her ability to protect the asset so long as they thought the asset wasn't going to recover. Now that Chuck was awake, they would no doubt reassess the situation. She had allowed her asset to be injured. Worse, her asset had been injured protecting her. In her grief and guilt after the incident, she had been foolish enough to admit that fact, something even Casey had conveniently omitted from his official report. Her record so far would keep her from being canned, but she was no doubt looking at a series of low-level, back-water assignments for awhile until she could prove herself again. Unfortunately, while she desperately did not want to leave Chuck, especially now, the rational part of her told her that she had obviously hopelessly compromised her mission and it would be better if another agent took her place.

She looked at Ellie to see Ellie studying her thoughtfully. Evidently her musings were evident on her face. "You can't blame yourself," Ellie said. "I know you are. I can see it. I told you before, Chuck loves you and he would do anything for you. I know he's glad that it's him lying in that bed instead of you."

She reached out and gave Sarah a hug. "I know that you and Chuck have, as you keep telling me, a 'complicated' relationship. I don't pretend to understand. But I want you to always remember, no matter what, you are now part of this family."

Sarah tried hard to stay professional. To stay the cool, aloof agent. But her damn eyes wouldn't cooperate and they filled with tears. She pulled Ellie into a fierce hug.

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While Chuck was sleeping, Sarah took the opportunity to go shower and change. She knew that she should also take the opportunity to stop by the Castle and report in to General Beckman now that Chuck was awake, but she couldn't bring herself to do it just yet. She feared an immediate reassignment or at least removal from the mission and she simply wasn't ready for that confrontation. She knew she was falling into one of the worst traps a agent could: ignoring a bad situation and hoping it would just go away. But after all that had happened, she just wasn't emotionally ready to deal with General Beckman. She would let herself revel in Chuck's recovery for at least one more day before the inevitable confrontation with her bosses.

She had just finished dressing when there was a knock at the door. She frowned. No one except Chuck stopped by her hotel (except, once, her father and since he was on the lam she wasn't counting on seeing him any time soon). She checked her pistol and went to check the door. She blinked in surprise. It was John Casey. Other than the Rajiv Amad case, she couldn't think of another time Casey had stopped by her hotel.

She slid the gun in the back of her pants, but kept her right hand close, just in case, and opened the door.

"Walker," Casey said and simply pushed past her into the room.

"Hello, Casey, come on in," she said sarcastically.

"You know, you really did screw the pooch on this one, Walker."

Same old blunt Casey. "Don't you think I know that? I told Chuck to get down, but he…"

"I'm not talking about that," he cut her off. "We need to chain him to the car so he'll stay. I mean why the hell did you tell Beckman that Chuck got shot trying to protect you? Now both our asses are on the line."

Sarah sighed. So much for avoiding the inevitable fallout. "I wasn't thinking straight," she said. "I… I'm sorry, Casey."

"Sorry don't feed the bulldog," Casey said. "You need to fix this." Without another word, he turned and stormed out of the room.

"Well," she sighed. "At least he waited until Chuck woke up."

She shook her head and went into the bathroom. She looked, frankly, like shit. Stress, fatigue, lack of exercise, and lack of proper nutrition had taken their toll. She was gaunt and hollow-cheeked and there were dark circles under her eyes. Now that the long vigil waiting for Chuck to awaken was over, she felt completely drained. She felt tears welling up in her eyes again and angrily brushed them away. What happened to the tough-as-nails agent that she used to be? How did she let herself fall so far?

With another sigh, she picked up her concealer and began to apply it to the dark circles under her eyes.

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Chuck was awake and had a tray of food in front of him when she arrived back at the hospital. A quick glance told her that he had merely picked at the food. She sat down next to the bed. "You have to eat something, Chuck," she said. "You're going to need your strength."

He smiled. "Well, isn't that the pot calling the kettle black," he said. "Ellie stopped by to get me to encourage you to start taking better care of yourself. Look at you. You're skin and bones. You can't be a kick-ass ninja assassin on an empty stomach."

She smiled at him. His voice was still a little slurred and he tended to pause before certain words, but it was good to have Chuck back. God, how she had missed their playful banter.

He reached over and took her hand. "Promise me that you'll take some time for yourself," he said. "Get some decent rest. Start working out again. I appreciate all that you've done for me, but now it's time for a little Sarah time."

Sarah felt herself blushing at his words. It was so like Chuck. Here he was still lying in bed with a bullet hole in his shoulder and less than 24 hours out of a coma and he was worrying about her.

"I promise," she said. She felt like she should pull her hand away, to start to re-establish the professional distance, but couldn't force herself to do it. "Isn't it about time for your appointment with Doctor Parker?"

"Yeah," he said. "The nurse's assistant y stopped by to tell me that she would be by…"

The door to the room opened and a striking middle-aged woman in an expensive suit and a white lab-coat stepped into the room.

"…right about now," Chuck continued with an ironic smile.

Sarah stood and faced the newcomer. She suddenly felt very self-conscious about her appearance in the presence of this very attractive doctor.

"Good afternoon, Mister Bartowski," the woman said. "I'm Doctor Andrea Parker. I'm the neurologist assigned to your case." She turned to Sarah. "And you must be Agent Walker." At a startled look from Sarah, Doctor Parker said, "Diane Beckman sent me a copy of Mr. Bartowski's file. I was called in as a consultant after Mr. Bartowski received the Intersect as to how the stored data would affect his neurological function." She turned back to Chuck. "I must say, you are a remarkable young man."

"Thank you, Doctor," Chuck said.

"Please, call me 'Andi,'" the woman said. "After spending so much time reviewing your case and talking with your delightful sister, I feel like we're old friends. Well, let's take a look at you, shall we?"

She conducted a thorough physical examination. Sarah moved to excuse herself at the beginning, but Dr. Parker insisted that she stay. "Protocol requires that an agent be present for my examinations," Dr. Parker explained. "Something to do with a Dr. Zarnow."

After her physical examination and after asking Chuck a series of questions, Dr. Parker pulled up a stool to sit down next to the bed.

"Well, Mr. Bartowski," she said.

"Please, call me Chuck," he replied.

She smiled. "Very well, Chuck. All in all, you're doing pretty well. Your cognitive function is excellent for someone less than 24 hours out of a coma, and your motor skills are in the acceptable range. The post-traumatic amnesia is normal and not something to worry about unless the short-term memory loss does not resolve itself. As for the events leading up to your injury, you may never recover those memories, and I don't want you to be concerned about that."

"The next few weeks may be very difficult for you. I've come up with a regimen of speech therapy, physical therapy and occupational therapy. We would like to move you to a special secure facility approved by the NSA."

At the mention of an 'NSA secure facility,' Chuck grew agitated. "I am not going to a bunker," Chuck said angrily.

Dr. Parker frowned. "Bunker? No. This is a facility here in Los Angeles we use for treatment of sensitive and high-profile patients. It's not a bunker. We can just monitor access much more closely that at, say, a nursing home or standard rehabilitation facility. Your family and friends will be able to visit you, provided we are able to properly verify their security status. I certainly wouldn't call it a 'bunker.'"

"When Chuck first received the Intersect," Sarah explained, "The NSA threatened to lock him in bunker… for his safety."

"How barbaric," Dr. Parker said. She shook her head. "The CIA has arranged for you to be classified as a research test subject, which is the explanation for all your bills being paid and for why you are at such an exclusive facility."

"So I'm a guinea pig?" Chuck asked.

"Mr. Bartowski… Chuck… You've been a guinea pig since the moment that you received the Intersect. No one has ever had such a volume of data downloaded into their brains. Frankly, it was not anticipated that anyone ever would. As I understand it, the whole idea behind image encoding was that an agent would review the encoded image relevant to their particular mission, not that anyone would see every image from the entire Intersect Database."

"Be that as it may, your recovery regimen will follow a standard therapy schedule for head injury cases of your type. We will simply also be monitoring you for how the injury has affected the Intersect data and your ability to… what is it you call it… flash?"

Chuck nodded. "Flash," he confirmed.

Dr. Parker nodded and continued. "Now, I have reviewed your MRI and CAT scans. There is currently an area of scarring… a brain lesion… that we are going to have to monitor. We're hoping that it will resolve itself over time, but brain injuries are still an area we don't know everything about. It's impossible to study brain lesions and the like without causing more harm by the invasiveness of the procedure to study the abnormality."

"Now, I want to go over what you can expect over the next several weeks or months. You may experience headaches; trouble remembering, concentrating, or making decisions; fatigue or a general feeling of tiredness; feelings of anxiety, listlessness or sadness; and irritability. We will be monitoring for more severe reactions such as seizures, which are possible in cases such as yours, but I wouldn't concern yourself over the possibility."

They spent the next several minutes talking over the specifics of the treatment until Chuck started to yawn again.

"Am I boring you, Chuck?" Dr. Parker asked. "No, no, don't worry, neurologist humor. It's actually very common for patients waking up from a coma to need a lot of sleep. As long as we monitor you closely for any sign of relapse, we should be okay."

Sarah and Dr. Parker left the room to allow Chuck to rest, and stopped in the hallway to talk.

"I wanted to talk to you privately, Agent Walker," Dr. Parker said. "Two potential side effects of brain damage are emotional instability and personality changes. Since we, meaning the therapy team, do not have a baseline it is impossible for us to monitor for these symptoms. We therefore are going to rely on you and Ellie – Doctor Bartowski – to let us know if you see signs of changes in his personality or emotional stability."

Sarah nodded. "I will, doctor."

"Good. Now, let's talk about you."

"Me?" Sarah asked, startled.

"The role of caregiver for a brain trauma patient, which is a role Ellie has informed me that you have taken upon yourself, is very difficult. First of all, it's emotionally and physically draining. The patient has a tendency to lash out at their caregiver in their frustration over the course or progress of their treatment. It can be an extremely difficult proposition, especially given the mood swings and irrational irritability of the patient."

"I understand," Sarah said.

"Actually, I don't think you do," Dr. Parker said. "I mean no offense by that, but no one who hasn't gone through this can really understand what they are getting themselves into. You are going to need your own network of family and/or friends to help you through this, as well. You are going to have to force yourself to get proper rest, exercise and nutrition. Especially an agent such as yourself if you are going to keep yourself in proper condition." She looked Sarah over. "Something I can see you haven't been doing." Sarah started to protest, but the words died in her throat. No doubt Drs. Parker and Bartowski had already had long talks about both Chuck and Sarah.

"I… I understand," Sarah said.

"Good, Agent Walker" Dr. Parker said. The kind, caring physician façade was gone and a hard-as-nails NSA asset stood before her. "Because I am going to monitoring you as well as Mr. Bartowski. And I will not hesitate to call your superiors if I believe that you are jeopardizing yourself or Mr. Bartowski's recovery, is that clear?"

"Very clear," Sarah replied.