A/N: Sarah had been resisting her feelings for Chuck, but when they only had seconds to live, a kiss was irresistible. Unfortunately, they were spotted and reported.

This starts in canon, but that one change causes a shift of direction. It will run parallel to canon, so events in Chuck's spy life continue. The story will eventually become happy Charah, but not for a while.

I know I have stories in progress, but this multi-chapter one has been swirling around in the depths of my mind for a while and has forced its way to the surface.

No betas involved, so if you spot any mistakes you feel need to be corrected, send me a PM.


Separation

Chapter 1


For a couple of months, she'd been fighting her feelings for him.

In the past, she'd always been in control, always the perfect spy, never letting emotions rise to the surface, burying them deep. Then she came to Burbank.

Initially, she'd thought it was going to be a quick and easy mission, but that soon proved to be wrong.

After the phone fixing ruse, she was going to use mild seduction to get him to take her to where he had the Intersect stashed and get him to hand it over, but she didn't achieve that. He was distracted by a dad who'd messed up and he focused on helping him and his daughter, ignoring her completely.

She watched in amazement at what enfolded before her.

Being unused to emotions, she hadn't recognized the flutter in her chest as he told the girl that all the best ballerinas were tall. She'd been rejected from the after school ballet classes when she was young for just that reason.

She had to try again in order to prevent the NSA getting to him. The date was the best of her life. Admittedly, it wasn't a real date, but then none of her previous ones had been. They were either mission ones with the scum of the Earth or cover ones with partners. This was neither of those.

She guessed very quickly that he was not in league with a rogue spy. He was an innocent caught up in this mess.

What had then ensued with him and Casey from the NSA seemed like pure fiction. He surprised both agents and saved the day, even though he didn't have to. It was what he did regularly after that.

Chuck Bartowski was an amazing guy. He was constantly fearful for his life, but willingly risked that to do the right thing. Or at least, what he thought was the right thing.

It was a constant source of friction between them that he would put himself in danger for her. No one had ever done that before and it unnerved her. It also brought those emotions forward. Emotions that she didn't know how to handle. She found herself lashing out at him because of her inability to cope with them, or sometimes even recognize them.

He was clearly enamored with her, and she realized that she was in the same state. Feelings she shouldn't have we're forcing themselves to the surface. She knew that if Casey saw her do anything inappropriate, she would be reassigned in no time. So, she desperately tried to bury those emotions.

Then they had a failed attempt to shore up their cover relationship and he'd upset her by likening her to a prostitute. She'd worn what she was sure he'd like to see her in, but that backfired. However, it was lucky that she was there, when it turned out that his sister had been drugged.

Later that day, Chuck acquired the only vial of antidote after he, Sarah and Casey had been dosed, and he refused to take it, giving it to his sister instead. It was typically him. As usual, he worked out where to find the felon and they managed to get the antidotes that they all needed.

What ensued was demonstration of another of Chuck's characteristics. He wasn't just clueless in the spy world, he was also incapable of realizing where he could talk openly and where not. So, in front of Casey, he stopped her taking the antidote and said, "This will probably be the last chance that I have to know the truth. I know you're just doing your job here, but sometimes it feels so real, you know? So, tell me. You and me. Us. Our thing under the undercover thing. Is this ever going anywhere?"

She was able to resist the truth drug, and could lie to him, much as she hated doing so. She could also feel Casey's eyes on them. However, the question he asked didn't need her to lie. "I'm sorry, Chuck. No." Much as she'd like it to, she couldn't see it happening.

Chuck slumped slightly. "Got it. Thank you for being honest. Even though I guess you don't really have a choice in the matter." They both drank the antidote and said no more.

Sarah hated the defeated look on his face, but felt they'd dodged another bullet.

The following day, Sarah's world fell apart.

Chuck unexpectedly came into the Wienerlicious. He looked nervous and she guessed he was still upset from the day before. He walked close to her and started talking. It felt rehearsed. "Sarah, you know when you think you're going to die, and your whole life is supposed to flash in front of you? That didn't exactly happen for me yesterday. In fact, mostly it was just a list that I saw. A list of stuff that I haven't done and things that I haven't had a chance to say. So today..."

He stepped even closer. "Today, I want to start crossing things off of my list."

Oh god! He's gonna kiss me. I want it too and no one is here to see it.

"And this is the first thing that I promised myself that I'd do." He was so close now and she almost puckered up her lips for what she'd been wanting for a while now. "We need to break up."

That broke the spell like nothing else could. "What?" she asked as it hit her.

Chuck rushed on. "You know, like, fake break up our pretend relationship. I just can't do this anymore, you know?

"The longer we keep trying to fool people into believing that we're a real Couple..." God I wish we were, she thought. He continued, "The person I keep fooling the most is me."

She could feel her eyes starting to water and looked down so he couldn't see that.

He walked out and she felt like he was walking out of her life, even though he couldn't because of what was in his head.

He immediately walked to the deli, while Sarah remained stationary, totally stunned. However, Sarah received a call from Casey breaking her out of that. "Yeah," she answered.

"I meant to ask you," Casey said. "When you were affected, did you say anything to compromise yourself?"

Sarah couldn't understand why he asked that. He was there and heard that she did quite the opposite. However, she wasn't quite herself and answered, "Uh... No. But if I hadn't been trained to withstand pentathol, I might have." As she said it, she cursed herself.

He just grunted and ended the call.

Sarah knew that was a stupid thing to say, but maybe it would result in what seemed to be happening, anyway. Chuck would start dating that Lou girl and she would be dispatched for being compromised.

She stepped out and looked over at the deli. He hadn't wasted any time. He was sitting at a table in the window and Lou was sitting opposite him. Both looked incredibly happy.

The tears were really welling up as Sarah turned back. Maybe this was for the best, she thought, awful though it felt.


Things with Lou didn't work out for Chuck. That was because she was involved with a smuggler called Stavros Demetrios.

Stavros and his father, Yari, were involved in bringing something dangerous into the States, and Lou seemed to be involved in some way.

Chuck had to follow her and got into an argument with her about cases she had received.

Sarah and Casey had been listening, but then lost signal and she rushed in. She and Chuck got caught and she found out that he'd ditched his watch to avoid them hearing more and Lou getting into trouble. That made her so mad.

Eventually, they were tied to chairs and faced Yari Demetrios who was threatening to plunge an electric drill into her head to encourage Chuck to talk. Yari handed the drill to another man who switched it on and approached her. She was breathing rapidly while waiting to be tortured, but she had gotten to one of her knives and was desperately cutting away at the thick rope around her wrists. She just hoped Chuck could keep quiet. She'd expected to die at some time. Him seeing it was her only regret.

Chuck must've flashed because he started babbling about the man approaching her, just before the drill touched her face, which stopped the man. Then, Chuck started on about one of the others. The two men started to argue and the drill was dropped as both drew guns. This ended when Yari shot and killed the second man.

Then another henchman interrupted with news about the dangerous shipment due to expire soon. Chuck obviously saw what the man showed him and flashed again. He told Sarah that he thought the package contained a bomb or a chemical weapon.

The brief respite gave Sarah enough time to cut through the rope. She'd seen Casey approaching and thought they had a chance.

She kicked the gunman away, then kicked Chuck's chair away as hard as she could to get him to safety. She then followed him, covering him from gunfire while she worked to free his bindings.

Casey appeared, firing his gun, and saying he would hold down the fort while she and Chuck went to find the bomb.

The pair of them ran out of the warehouse; Chuck lagged a bit behind while he was undoing the ropes on his wrists. Sarah told him to get away from the area, but he refused.

Sarah stopped running and grabbed his wrist, stopping him, too. She told him to stay away from a live bomb.

That was one of those moments of bravery from him. He pointed out that he had the Intersect and that they needed it to defuse a bomb. He was probably right, but he ran ahead and she had to follow.

When they finally found the right location, they discovered an enormous wooden crate, about eight feet high, ten feet long, and six feet deep. Sarah spotted two crowbars on a rack and grabbed both, tossing one of them to Chuck.

Together, they pried the front of the crate off, to reveal a long gray, metallic cylinder that had a timer on it, counting down in flashing red numbers. There was a minute left.

Sarah went straight to the panel and pulled it apart to see if she could discern which, if any, wires to disconnect.

She asked Chuck if he'd flashed, but he hadn't. He started babbling.

She told him to go, that she'd stay and try to defuse the bomb, although she knew that was hopeless.

"No, I'm not leaving you here," he said defiantly. He was staying to die with her.

She angrily ordered him away and he refused again.

She lost it at that point, really wanting him to live, although the reality was that he'd never get away from this. She stupidly drew her gun on him. He pointed out how ridiculous that was, threatening to shoot him so he wouldn't be blown up.

"Why are you so stubborn?" she hissed.

"Actually, I consider this a rare moment of courage. I don't know where it's coming from. I guess you just bring out the worst in me," he growled.

She put her gun away, still mad and almost in tears over the fact she'd failed to protect him and he was now going to die. She took a threatening step towards him. "And you in me," she snapped. In reality, she knew he actually brought out the best in her, but was too angry to say that.

The beeping of the timer, ticking away with ten seconds left, distracted them. "It was nice knowing you," he said and closed his eyes. He seemed surprisingly calm while facing death.

She suddenly desperately wanted to kiss him, really kiss him. With four seconds left alive, she stood on her tiptoes, grabbed his face, and kissed him hard.

It obviously surprised him and it took him a second to respond and kiss her back. His lips were soft. It wasn't like a cover kiss, not at all.

She reached behind his head with one hand and grabbed a fistful of his shirt with the other to hold herself up on her tiptoes. She felt his arms reach around her, lifting her off her feet and crushing her against him.

This kiss was certainly one of people expecting to die any instant and savoring the last moment together. For Sarah, no kiss had ever been this good. It was definitely passionate. As soon as she opened her mouth, his tongue was wrapping around hers. No one had ever kissed her so well, and she'd never kissed anyone the way she kissed him back. For her, time stopped moving forward. The bomb and death were forgotten completely.

After a while, she wondered if she'd died and this was heaven, but knew she'd never end up there. That brought her back to reality. The bomb should've gone off and obviously hadn't.

They stopped kissing at the same time. She reluctantly pulled her lips away and opened her eyes, realizing that they'd had been closed through the best kiss of her life. He was now looking at her as he gasped for breath. The emotions visible in his eyes made her feel faint.

She wanted more kisses like that, but knew that couldn't happen. She dropped to her feet and they both looked at the timer, set at all zeros. Nothing had happened.

Struggling for breath herself, she said, "Well, the good news is, we're alive." He looked away. "And the bad news is that this is kind of an uncomfortable moment right now." She felt the happiness and regret battling inside her.

Chuck made that worse when he said, "It's completely comfortable on my end. Just saying."

She'd felt like she was floating on air during that magical kiss, accentuated by the fact that he'd lifted her off of her feet. But now, she felt like she'd crashed to the earth, faced with having to backtrack and convince Chuck that it was a mistake that couldn't happen again. He needed to understand why that was or he'd persistently try for more, and she'd struggle to resist.

Then, she heard movement near the entrance and quickly looked that way. Armed men were moving in around one that stood motionless. Casey was glaring at them with one hand holding a gun pointing down and the other holding that arm.

She knew instantly that she was doomed, which was emphasized by Casey swiftly turning and walking away.

She looked back at the man only feet away from her. Chuck was still looking adoringly at her, oblivious to her fate.

With a sinking heart, she said, "We should go and leave this to others."

She walked to her car with Chuck silently walking beside her. Once seated inside, she quickly set off. Before he could say anything, she had to talk. "Casey saw us," she quietly said.

"Saw you kissing me?" he questioned.

"Yes."

"It was the best kiss of my life," he said as he sat back.

Knowing the cover was blown, she admitted, "Mine, too."

He chuckled. "It's good that Lou dumped me, then."

She pulled over and stopped the car just before they left the docks completely. "Casey will report it to the general, who will tell the director."

"Is that a problem?" he asked.

"Handlers are not allowed to have relationships with assets."

Realization hit him and he looked concerned. "So, you'll be in trouble?"

"More than that, Chuck. I'll be sent away." His jaw dropped. She clasped his hands. "That's why I don't think we have a future together."

She felt the tear slip out and trickle down her cheek. He reached up and brushed it away with his thumb. She couldn't stop herself from leaning into his palm.

"How soon?" he asked.

"Depending on when he tells her, maybe as soon as tomorrow."

He gasped. "That soon?" She just nodded. "Why did you kiss me?" he asked.

She looked down at their hands, now linked across the center console once again. "I couldn't die without knowing what really kissing you was like. It was a mistake that will now result in me being sent away."

"They may not-" he started.

She cut him off, not wanting him to raise his hopes or try to raise hers. "They will. I broke the rules."

He slumped down and let go of her hands. She just looked at him. It was like she was trying to memorize his features. He glanced back at her, taking in her features, too. "I wish you hadn't kissed me now, but at the same time, I'm so glad you did."

She felt just the same. "Stay with me tonight?" she softly asked, nervous that he'd refuse.

"Our last night together?" he asked. She nodded, biting her lower lip. "How can I refuse?"

"Thank you, Chuck. Something for me to cherish when I've gone."

He nodded and stayed quiet for the rest of the journey.


They stopped in Echo Park for him to collect some things and to let his sister know what was happening.

Once they reached the hotel, they walked side-by-side, holding hands from when they left the car until they reached her room.

Once inside, both were subdued. They took it in turns to use the bathroom before climbing into bed. She wasn't wearing anything provocative, just pajamas.

It was like they'd done this before, with both gravitating to the center and holding each other. This was what she'd wanted their night in his room to be like but had messed up with what she wore. An even bigger difference was that there was no recording active. It was just the two of them together, for real this time.

Even though she hadn't been told yet, she felt like these were their last moments together. She let her emotions take over and clung to him. She knew that was selfish. It would make the parting so much more painful, but he was the first man who'd made her feel like this.

He held her just as tightly. "I'll never forget you, Sarah Walker."

Those words cut right through her. She felt the same about him, crazy though that was after so little time together… but not really together. How could someone affect you so much, so quickly?

Neither spoke after that. They just stayed together, neither wanting to separate.

Eventually they fell asleep like that.


A/N: So, together… for a while. Obviously, that's not going to last.