A/N: Thanks for sticking with this very different Chuck story. I know a lot of people don't like science fiction (even though Chuck is partly that), so I'm not surprised that numbers are down on this. I really appreciate those that made time to leave a review - thank you.

Note that this Intersect, does have more to it than even version 2 in canon. It provides skills, at the request of the user and, as we saw, could be told to suppress feelings (Laudanol-ish).

MicroGirl1225 again kindly pre-read this for me. Thanks.

This chapter is the aftermath of Chuck's actions along with their rescue. It is effectively the final chapter of the first arc, but there's definitely more to follow.

Far Distant Chuck

Chapter 5

Having Chuck Bartowski pressed against her in the state he was in from killing all those men caused Sarah to remember the first time she had killed anyone. It had been a horrible experience.

She'd risen through the ranks very quickly due to a combination of skills and abilities. She was totally focused on achieving her goals, and a skilled tactician, but actually killing people was one of the worst things she had to do. No one had comforted her. It was part of the job. She had to just get over it or she'd be out. She'd do it, just as she had here, but had to bury the memories of it, as thinking about it afterward haunted her.

In those early days, they came back as nightmares, waking her. In order to function, she had learned to bury them deep in the back of her mind.

Could she train Chuck to do this? Unlikely, she thought, and she wouldn't know how, anyway.

His situation was different. He hadn't killed the men, the Intersect had, but the memories were still there.

He was still sobbing and she was still holding him, his mask pressed against her just under her chin.

She'd certainly never done this before. Her peers when training had to just cope or leave. The men and women who reported to her had learned how to cope by the time they joined her.

She'd never had to comfort civilians either.

That wasn't the only aspect of this new experience. She'd never cared for anyone before, wanted to make them feel better like she did with Chuck Bartowski. She was pretty sure she'd be better off without such feelings.

Chuck stepped away from her, she had to stop herself from laughing. His mask was a mess. A combination of liquids from his eyes and nose were smeared over it.

She said, "Hold your breath." Then she reached to the right side of his mask and pressed just behind his ear.

His face disappeared completely as the plexiglass was coated in cleanser and then cleared.

"I didn't know it could do that," he said.

"Obviously not," she replied.

She didn't manage to hide her amusement, because he said, in an accusing tone, "You're laughing at me."

"I'm not!" She exclaimed. "But it was hard not to, with the mess your mask was in."

He huffed.

"Stay in the lab," she advised. "I'll clear up out there."

He shuddered as he thought about what was in the corridor, and sat down to wait for her.

She went out, holding her laser. She'd use that on the various body parts.

Chuck sat and pondered what they should do about the Intersect. It was still something that The Force would want to attain, so, if they didn't destroy it, there would continue to be a threat associated with it.

He also was struggling with the idea of handing it over to the Republic. What it provided would be irresistible to their military and politicians, and they may abuse the technology, too.

Everything pointed to the best option being its destruction, along with the plans. Could he persuade Sarah to do that?

He couldn't ignore the fact that without it, both of them would be dead now. Sarah would've died first. That thought made him shudder. She had become so important to him that the thought of losing her that way was awful.

Of course, once they were back in civilization, they'd separate and he'd lose her anyway, but at least he'd know she was alive.

Sickened though he was at what he'd done, having saved Sarah made it easier to accept. He knew he'd have nightmares, but she was worth it.

That led him to thoughts of the continued fight against The Force. Even if they destroyed the Intersect, The Force may not believe it and would come after it. That meant he would still be at risk, as would Sarah.

He was coming to the realization that he should not only keep it intact, but also hold onto it. He thought he could trust Sarah to use it, but no one else.

He had to work out how to hide it and sat thinking about that until Sarah rejoined him.

Sarah walked back into the lab. She had removed the evidence of the fight, so she would not have to explain what had happened to that level of detail.

She'd been thinking about this while away from Chuck and what to do about the Intersect. She had to talk to him before they were rescued.

Lieutenant Fraxier had told her the ship would arrive in just over an hour, so there wasn't much time for discussion or to put a plan into action.

She was pleased that Chuck seemed to have put his actions behind him, or was at least ignoring it.

"They'll be here in an hour," she told him. She took a deep breath before launching into the key discussion topic.

"About the Intersect-" both said at the same time. They both halted and a wry smile appeared on each of their faces.

"You've been thinking about it, too?" he said.

"Chuck, I think it's too dangerous to let anyone have it."

She watched his reaction, glad that she could see his face.

"I agree," he quietly replied. "But-" He halted and looked nervously at her before continuing. "Without it, I would've lost you."

They would both have died, but his words told her what was most significant to him. "We would both have died, Chuck."

"Yes, yes," he rushed out. "But for me, the fact that I could contribute to our partnership was significant to me."

She suspected there was more to it than that, but shied away from those thoughts for now. "Thank you, Chuck, but I think you were already contributing a lot before that."

He took a deep breath. "I don't want to destroy it." She opened her mouth to respond, but he rushed ahead. "The Force will not believe we've done that and will come after us."

Sarah made the mental connection. "You want to keep it to protect… us."

"I do," Chuck replied.

Sarah was sure that he just wanted to protect her, which made her feel strange. It wasn't uncomfortable, but certainly not something she'd experienced for a long time. However, the recent experience confirmed that she couldn't take on The Force on her own.

When she was back with her team, she would be able to, but would then probably be separated from Chuck and he would be vulnerable. Why did that upset her so much?

"If you keep it, you'll need to keep it hidden, but we won't be able to stay together," she pointed out.

"I know," he said, looking sad.

She felt equally sad at that thought.

The mask folded down more than it was when they found it, so it was relatively easy to hide on Chuck's person.

He archived off the plans for the Intersect and the other devices, and hid that in a pocket, too.

They decided to take the amazing gun before setting the explosives in the lab and sealing it.

At the front of the building, they set off the explosives remotely. The explosion shook the building and after ten minutes, they went back to check on the lab. The door was blown off, and they were able to enter easily. Everything was destroyed, as they'd hoped.

Chuck felt sad at all that was lost by doing this, but he knew it was the right thing to do.

"It was fortunate that you didn't mention the lab or its contents," Chuck commented.

"Mmm."

Chuck could sense her tension. "Are you alright, Sarah? Do you feel like you are betraying the Republic?" He saw her wince and regretted his wording.

"Yes," she tersely replied. "But it's the right thing to do." She looked him in the eyes. "I'm not sure about you holding onto it, though."

"I'm possibly the best person to study it," he replied. He could see that she wasn't sure about that, but she did know that he would keep quiet about it.

"Will I see you after we get back?" he asked. Somehow, this was very important to him.

"I will request that you are protected."

That didn't answer his question, but her look suggested he shouldn't ask again.

They watched the large spaceship landing and Republican men alight on the planet. The two of them set off toward it.

"Captain," the first said as they met.

"Lieutenant Fraxier, this is Chuck Bartowski. He helped me."

Fraxier looked at Chuck with a certain amount of respect, something Chuck hadn't expected.

"We found the Intersect but had to destroy it when The Force team destroyed our craft and looked to be about to beat us."

"How didn't they?" Fraxier asked.

"Chuck used this weapon on them," she replied, showing the gun.

The respect Chuck saw increased.

"We need to destroy the buildings completely before we leave," Sarah said. "We want this to look like that was the result of The Force invasion."

"Very well, captain. You both go and get those masks off and breathe some real air again. I'll organize things here," Fraxier replied.

Sarah led Chuck to the craft. As he walked there, he wondered if Fraxier and the men would check the building to see if Sarah's story was true, but he knew better than to ask.

Sarah had to admit that it was good to have her mask off.

Obviously, Chuck felt that even more than her, but his gasping as he removed his was still comical. She couldn't hold in her laugh, which elicited odd looks from her team. The ever serious Captain Walker never laughed.

She got herself under control, noting that she needed to behave normally or she'd lose the respect that she'd attained over the years as she rose to her current rank.

She told Private Jane Jackmon to take Chuck to one of the cabins and to show him where to clean up and find new clothes.

After watching them walk away, she turned to Lieutenant Palak Gulax. "Did the following Force spaceship send any messages out?"

"None that we captured," he replied.

"Are there any others on the sensors?"

"No, Captain."

She knew that didn't mean The Force weren't coming, but it was a relief, all the same. "We should still get away as soon as possible," she replied.

Gulax nodded.

"I'm going to have a shower. When Lieutenant Fraxier returns, tell him I want us heading to Republic Central."

She headed to her cabin and that shower.

Chuck felt more normal after a shower. Having said that, there was no way to scrub the feeling of blood on his hands. The blood of all the men that he'd killed. Visions of the blasts from the gun blasting through them and the remains of the limbs falling to the floor appeared in his head as he stood and used blasts of water jets in the shower in the cleansing process.

He guessed that these memories would stick with him for some time, if they ever left him.

He decided to ask Sarah how she coped, at least with her first kills.

Chuck knew she presented a tough, hard, even, no-nonsense image to her men, but he felt that was a mask and the real woman underneath had shown herself occasionally to him during their time together. A woman she hid from others, but that he'd been privileged to see. One that wasn't so immune to the horrors she experienced. Could she teach him how to bury it?

Jane had told him to stay in his cabin after his shower. He suspected that was because she didn't know what else to say, but probably didn't want him just wandering around.

He sat on the bed, wondering if he was a prisoner here, but wasn't going to risk getting into trouble, or more significantly, getting Sarah into trouble.

He didn't really know Sarah's position on board. Was she the captain of the ship? He didn't think so. She was captain of a team of men, not of a spaceship. So, who was the ship's captain? And what was her situation on board?

There was a knock on his door. "Enter," he responded.

The woman in his thoughts walked in. She looked like she had when he'd first seen her. Formal, with that severe hair-style. It made him realize how that had slipped during their time together. She was still stunningly attractive, but less welcoming.

"Have you settled in?" she asked.

Chuck gave her a rueful smile. "Not sure if I'm a prisoner in this room, or not."

Sarah's mask slipped slightly. "No!" She then sighed. "I didn't tell Private Jackmon what to do with you. You can't come into the control room unless invited. You'd be in the way, but apart from that and other cabins, you can probably go most places."

"Can we talk?" he asked.

She hesitated momentarily but then nodded and sat on the chair by the desk.

"What's going to happen to me?" he asked.

"What do you want to happen?" she responded.

That was a rather irritating non-response. He frowned at her. "Don't reply with that! I want to know what will happen to me when we return to the Republic. Will I be free or not?"

Sarah sighed. "There's no reason for you not to be free, is there?"

He tried a different tack. "Will I be safe if I returned to my home planet?"

She looked surprised and something else. Was that disappointment? "I don't know," she replied. "Is that what you want to do?"

He decided to say what he wanted to do. "I'd rather be with you, but I'm sure that's not an option."

The look of panic in her eyes meant something. It suggested that what they said might be overheard. He hadn't thought about that. His words could get her into trouble, even though nothing had happened between them. Before she could respond he tried to correct his mistake. "Besides, that's just me wanting something I've never had. A beautiful girlfriend."

Her panic seemed to ease. "Chuck, I've given you no indication that could happen. I'm not that type of person."

He sighed. "I know."

"I will take you to the Council. They may know a way for you to be safe on Paldane, your home world, without Republican protection." After saying that she stood and he guessed the conversation was over. "Come. I'll show you the places on the ship that would be relevant to you." She turned and walked to the door and he had no option but to follow.

She led him around, showing him the library, where he'd be able to learn about the worlds from a guard point-of-view, the restaurant area, and the viewing deck.

"Will I see you again?" he quietly asked as they walked back to his room.

The fondness was evident in her eyes as she looked at him. "I know you're probably still shaken up after what you did. Call me if you want to talk."

He then thought to ask what he should have done before. "Are you in charge here?"

She sadly nodded. "I'm the most senior person since the ship captain and his executive officer were killed by The Force when we landed on Paldane."

That seemed odd. "But doesn't the command fall to the next navy officer?"

"Running of the ship does, but overall command shifted to me."

He shook his head. "I'll never understand the Republican guard way."

Outside his room, she seemed to maneuver them in a particular way and stopped him. "Chuck," she said and placed her hand on his arm. "Seriously, the first kill is difficult. Call me if you get nightmares. I'll come."

"Isn't that inappropriate for the commander?" he asked, appreciative though he was.

"No one else knows you. I think I'm best… if you need it."

There was more in her eyes, but he couldn't ask. He just nodded. "Thank you."

Sarah had told the watch, the medical officer, Lieutenant Janet Adams, and Lieutenant Fraxier about Chuck's likely need for her overnight. None looked surprised, nor did they question why she would go.

The sensors in his room were directed to Sarah's display and audio.

She didn't undress to go to bed, because she awaited the summons, either requested or through cries.

She was just dozing when she heard Chuck's cry. He must've been asleep for less than an hour. She leaped out of bed and hurried to his room. His room access included an override that accepted her.

In no time, she was crouching beside his bed and leaning over to the thrashing man trapped in his nightmare. Without any hesitation she wrapped her arms around him and whispered in his ear, "I'm here for you, Chuck."

She didn't see his eyes open, but believed that he'd woken as he gripped and hugged her tightly and he seemed to calm down.

"Sarah! I saw them dying again, but their heads didn't vanish, they stayed and stared at me! Then, you looked around and stared in horror at me, just before a laser bolt shot through your chest!"

He thought he'd failed! "I'm still here, Chuck. You saved me."

He clung to her.

Sarah was caught up in his nightmare! She should've expected that, but it was unnerving.

She hoped that these nightmares would ease, as hers did, but she couldn't help wondering how he would react when they went their separate ways and she was out of his life for good.

She had a horrible feeling that she was going to miss him and he had stated that he didn't want to be separated from her. However, she couldn't see a way for anything different to happen. As he'd said, he didn't fit in the life she led.

The thought of him suffering nightmares of her dying when they did separate in a few days made her feel so upset. Maybe he wouldn't. She clung to that thought as tightly as he was clinging to her.

Chuck woke up and felt completely disoriented. He wasn't alone in bed!

He was clinging tightly to someone else, and he recognized her scent. Captain Sarah Walker! He remembered his nightmare and a conversation with her which he'd thought was part of a dream, but apparently wasn't.

She obviously sensed him waking up and he released her as she sat up. She was clothed just as he'd last seen her. "Sarah?"

"You had a nightmare and I came to help," she replied.

He was confused, but the most pressing thought came through first. "By being in bed with me?"

She chuckled. "Not initially. I crouched by the bed and held you. We talked briefly and then you latched onto me before going to sleep again. I realized that holding someone was what you needed."

He couldn't resist smirking. "Is that what the commander does for everyone?"

Her jaw dropped. "I'm here for you, and you make a comment like that?"

He was ashamed. "I'm so sorry, Sarah. I do appreciate what you did. I take it that I had no more nightmares."

"No. You slept through."

He frowned. "Much as I'd like to hold you every night. It's not realistic."

Sarah sighed. "No, it's not." After a pause, she said, "I'm going back to my cabin to prepare for the day. Do you want to get ready and join me for breakfast?"

Chuck smiled. "How can I resist breakfast with you?"

She looked hesitant, then smirked. "No hand holding with the commander!"

She immediately turned and left him.

"Aww!" he muttered.

Chuck had another nightmare the following night. He woke in Sarah's arms once again. This time his desire for her and what had happened in the dream kicked in and he kissed her. She reacted quickly and pushed herself away, separating them. She looked shocked at him, as he fully woke up. "What…?" she cried out.

He focused on her and his eyes widened as he realized what he had done. "I am so sorry, Sarah. In my nightmare, you'd grabbed me as the limbs dropped to the floor, and I thought what a monster I had become and started bemoaning it. You kissed me to shut me up and I kissed back."

The shock was wearing off, and it was now amusing her. "So, kissing me is nightmare material, huh?"

He was pleased that she was no longer upset. "We can test it now that I'm awake," he suggested.

"I don't think so," she replied, looking serious again. She sat at the end of the bed. "And I'm not letting you hold me tonight, with you being like that. Go to sleep, Chuck."

He knew he'd miss waking up holding her, but he understood why.

He lay down and fell asleep wondering when she'd return to her own room.

Sarah had learnt, over her time in the guard, how to sleep anywhere. So, sleeping on Chuck's floor was no big deal.

She was woken by Chuck again, but this time, not because of a nightmare. He gasped and she heard it and sat up. "Sarah! You shouldn't sleep like that!"

She sighed. "Not with you waking me like this!" she grumbled.

"You should've pushed me over and slept on the bed!"

"Not with your grabbing hands and uncontrolled lips!" she growled.

He huffed. "I couldn't control them."

"I'm not sure I can trust you anymore," she replied. She wasn't sure she could trust herself, either, but wasn't going to mention that.

"I wouldn't ever hurt you, Sarah," he stated honestly.

She was sure that was true. The fact that she could overpower him fluttered at the back of her mind, but the fact that he cared about her was strong, and therefore her foremost thought.

Sarah partly wished that she'd not pushed away and had allowed that kiss to continue. Maybe even kissed him back. She had to bury those thoughts quickly.

She looked at the time. She should go and prepare for the day. Standing, she said, "Breakfast together, again?"

He nodded. "I promise not to try kissing you across the table."

She had to swallow her laugh and replied, "I would have to slap you, and then not be your support tonight."

"I'll be good." As she turned toward the door, he added, "I'll sleep on the floor tonight."

She turned back. "Think you'd sleep?"

"Probably not, but you shouldn't be there."

She sighed. "I can sleep anywhere. Trained to."

She left him frowning at that.

Sarah had arranged for a spare pillow to be taken to Chuck's room, saying that he complained with just the one and thought another might help him sleep. In reality, it was for her on his floor.

She decided to sleep there from the start, which resulted in an argument until she ordered him to go to bed and to sleep.

She could feel his eyes on her as she lay down, but quickly drifted off.

When she woke up, she found him still asleep and it was time for her to prepare for the day. He'd slept through the whole night.

"Chuck, it's time to get up."

His eyes fluttered open and gazed at her. It reminded her how good he looked when not stressed.

He then looked surprised. "No nightmares!" he said.

She doubted that he was over them, but didn't say that. "I'll go back to my bed tonight."

The disappointment in his eyes made her heart beat a bit faster. "But still breakfast together?" he asked hopefully.

She smiled. "Only if you set an alarm."

"I will," he responded as he sat up.

That night, Chuck woke up from a nightmare. He was sweating, but he was fairly certain he'd not cried out.

He lay on his back waiting to see if Sarah had heard anything and would come to his room. Several minutes later, she still hadn't arrived. A selfish part of him wanted to cry out so that the most beautiful woman would appear, but he squashed that thought.

He eventually drifted off again, only to wake with another nightmare.

At least these nightmares were Sarah-free. The fact that he'd not cried out was a bonus, too. However, after two more nightmares, all about an hour-and-a-half apart, he was getting fed up with them. He was also very sweaty, so he rose and had a shower.

Feeling better, he carried his pillow to where Sarah had been lying on the floor previously. Lying down, head on pillow, he imagined that he could smell her scent around him. It was unlikely, but a pleasant thought.

He drifted off to sleep and overslept.

"Chuck." Sarah's lovely voice woke him.

His eyes shot open. "Oh no! Have I missed breakfast?"

She smiled. "No, but you will unless you come immediately."

He checked the time. "I showered a couple of hours ago, so I just need to get changed."

She grinned. "You can tell me about the rest of your night over breakfast. I'll get what I've seen you eat each day, so get dressed and join me."

She walked out and he scrambled to get ready.

It took them eight days to get to Saggittarn, where the Republic Council resided.

Last night, he'd slept through without a nightmare and Sarah hadn't needed to come to him, as she hadn't on the previous nights when his nightmares hadn't resulted in loud cries. He was both pleased and disappointed, especially as he was unlikely to see her again after today.

Breakfast had been a somber affair. She seemed as sad about them arriving as he had. "Whatever happens, I will miss you, Chuck," she quietly admitted over the table. Her eyes looked watery as she said that. He'd obviously told her he would miss her, too.

So, they now faced the Council. He should regard it as an honor, but the sadness about separating from the beautiful captain stopped that.

Sarah told their story, with Chuck just answering questions.

One of the Council had commanded the men in the war and knew someone on Paldane. "He'd be safe if he stayed with Colonel Casey."

As Chuck heard the name, he thought about how life went in circles. He also wondered how Casey would react to this. Unlikely to be totally happy!

Now he was definitely leaving Sarah. He knew he was going to miss her terribly, but it had to happen. He looked over at her. She didn't look at him, just faced the Council, as a good guard would. Her professional mask was in place, of course.

He would briefly get to say goodbye to her before he left. He wished he could kiss her. Really kiss her, but knew that wouldn't be appropriate.

He just hoped that he would see her again sometime.

A/N: Yes, Chuck and Sarah are parting, but I promise that they will get back together later in the story.

It would be great if you could spare the time to leave a review. More important than ever with reader numbers so low.