A/N: While I was struggling with an alternative version of "Chuck vs The First Date" in my story "Piranha Vs The Intersect," I found myself wanting to write another different path for Chuck.

Having followed canon through the whole of season 1, this story now goes AU. I know stories like this have been written before, but here I'm sharing my take on it.

This will be 12 chapters and a short epilogue. It's all written and beta'd. So, thanks to CharmingCharles2896 who agreed to beta this for me.

When Chuck finds out about the kill order associated with the introduction of the new Intersect, he knows he has to run from the CIA and NSA. If only he knew whether he could trust the woman who'd stolen his heart.

Elusive Intersect

Chapter 1: Leaving

Chuck had spent the last three months taking out cash and putting it in the savings account his dad had set up "for a rainy day." When he was young, Chuck had wondered why there was an account in another name that they had access to. Now, he was pleased that his crazy dad had done it. The money Chuck added wasn't that significant, but it had kept the account active and him as the person using it.

Obviously, he'd been careful to erase recordings of him entering the bank each time.

The transactions themselves were recorded in the account booklet which he would present when he needed cash. Discovering the plan to "terminate" him when the new Intersect was activated meant he really needed that money. Chuck knew he could use cash in motels and small guest houses, so wouldn't need card payments.

Chuck had wondered if his beautiful blonde handler knew of the plans to kill him, but he wasn't going to ask. If she did know, it would alert them to his knowledge. If she didn't, she might try to avert it. The thought of her possibly getting killed was too awful to think about. He knew he was in love with her. How could he not be? To add another wrinkle, Chuck also thought that Sarah had feelings for him, otherwise why would she have kissed him in front of that bomb that wasn't a bomb?

He was sure that both Sarah and Casey would be sent after him. Sarah would do that out of a sense of duty, something she would find hard to resist, even if she wanted to. Would she shoot him on sight or capture him? If Sarah did capture him, would she take him back to LA or to DC? That would likely depend on whether she was ordered to kill him or not. Casey, almost certainly, would shoot to kill.

Tonight, the recording loops for all Casey's cameras would kick in as the taxi Chuck had ordered for Jake Blakeman would arrive and Chuck Bartowski would disappear. At least doing this while Sarah was away meant Chuck didn't have to see her, something that would have made it hard to just leave her at all.

Sarah was surprised how much she was missing Chuck. She'd been sent back to DC for recertification during the quiet time in LA, two weeks away from the man that Sarah found extremely difficult to treat as her asset. She would protect him with her life, that was her job. However, Sarah knew this was more than that.

She hoped that Chuck would forget her mistake when she thought they were both going to die. She'd let her feelings take control and really shouldn't have. What she'd done was unprofessional, but worse than that it had given Chuck the wrong message. Yes, she had feelings for him, but she couldn't act on them. It had caused problems between them when she'd tried to reset the relationship to a professional one, especially with Bryce appearing, but she thought that she and Chuck were now back to their old status.

Occasionally, out of the corner of her eye, she'd noticed Chuck looking at her with an almost melancholy expression. When she'd turn to face him, Chuck would look normal again.

These days, things seemed to be going smoothly in Burbank. There were no dramas to speak of, until then this recertification came up and Sarah was sent away from him. The recertification itself was hard work, it always was, but the evenings were when her mind drifted across the continent, thinking of that curly haired man with the lovely hazel eyes.

Sarah was nearing the end of her first week. She knew the weekend would be hard. Less to do, more time to miss him. So, far she'd managed to stop herself from calling him. She'd called Casey on Monday and Wednesday night, just to check in. Thinking back, Sarah remembered her last conversation with Casey ...

xxx

"He's focused on Buy More work, just as he was on Monday," Casey said exasperatedly. "And spending his evenings with his sister and her boyfriend, just like on Sunday and Monday."

"Have you talked to him?" she asked.

Casey grunted. "As little as possible. He asks about you."

Sarah smiled. Even though they couldn't have a real relationship, it still pleased her that Chuck seemed to be missing her as much as she was missing him.

"You keep him safe, Casey. He only has you," she replied. Casey was silent for a moment. That was a bit worrying. "You are still there with him, aren't you?"

"I'm still here in Burbank. Wishing I wasn't, but I am."

"Wishing you could be out shooting people?" she teased.

Another pause followed by a grunt. Then, he said, "Just focus on your recert, Walker. And no more calls."

xxx

Sarah wasn't going to call Casey again, but she was worried about Chuck. Was he safe without her? Maybe over the weekend, she'd call Chuck directly. She could claim it was because she was still his handler and his safety was her responsibility. Hearing his voice would help her get through the weekend. Maybe it would help Chuck to hear her voice too.

The surveillance loop was on, and the taxi would be arriving in the next minute. Chuck left via the Morgan door and quietly slipped through to where the car would arrive. He stayed in the shadows with his backpack of clothes, along with his laptop bag that also contained all the other equipment he might need.

The taxi pulled up and Chuck hastened to it. In an instant, Chuck was on his way. No turning back now.

He had mixed feelings. He was going to miss his sister, her boyfriend and Morgan. He'd left details for Ellie about what had happened. He'd advised her not to share that with others, for both of their safety. As another contingency, he'd set up a nightly trigger to send details to the media amongst others, if he didn't disable it. If anything happened to Chuck's loved ones, that information would get sent.

Chuck's greatest regret, however, was that he'd never see those beautiful blue eyes again, or that gorgeous smile.

He fully planned to monitor what happened back in Burbank, as well as follow the exploits of the amazing Agent Walker. If she and Casey were sent after him, he'd obviously follow that too, keeping ahead of them both.

This was going to be a hard life, but Chuck was determined to survive.

Of course, he was also going to work on the Intersect removal, so that maybe he could come out of hiding and catch up with his dream girl again, sometime in the future.

Sarah had been back at her DC apartment for almost an hour. She showered and was now in jogging pants and a t-shirt. One of Chuck's that she'd pilfered from his drawer.

She had tried calling Chuck, but gotten no reply. She thought that odd, but maybe he was having a gaming night with Morgan. It was Friday night after all.

She'd ordered a pizza to be delivered so that she at least filled her stomach with something good.

The knock on the door came at the right time, but she still called, "Who is it?"

"Pizza delivery," came the reply.

She sauntered over and opened the door and was shocked to see who was standing there holding the pizza.

"I took it off of him because we need to talk."

"I'm in no mood to talk to you, Bryce," Sarah said, snatching the box off of him and starting to kick her door shut in his face.

"It's about Chuck. He's in danger," Bryce said.

That stopped her. She looked into Bryce's eyes and did see concern there.

She nodded for him to enter, closing the door behind him. Putting the box on the table, she pointed for Bryce to sit. "Talk."

"Sarah, I know you well enough to realize you have feelings for Chuck and are trying to ignore them." She opened her mouth to argue, but he stopped her. "I'm not here to argue the point, but I say that because I think you are someone I can trust to talk to talk to about him."

She looked at him for a moment, then repeated her previous command, "Talk."

Bryce held her gaze as he said, "Graham and Beckman want him dead."

"What?!" she gasped out.

"They've been building a new Intersect," Bryce told her. "When they activate it, they'll download it into agents. They don't want another active Intersect in existence after that."

"How do you know this?" she hissed.

"Beckman let it slip about the new Intersect," he replied.

"But the rest is your conjecture?" she asked.

"Come on, Sarah. It makes sense." Unfortunately, it did. And it also matched Graham's attitude toward Chuck.

She hadn't known about the new Intersect, but if she had, she would probably have assumed Chuck would be dropped like a stone and she and Casey sent away. She wouldn't have thought about disposal of the civilian Intersect. She was obviously naïve, or just so focused on Chuck that she had blinded herself to that possibility.

"I have to get back to him," she declared, standing up.

Bryce laughed. "I'm the impulsive one! You always plan."

That halted her. She had no plan, just a need. Sarah slumped back into her chair. "Do you have a plan then?"

Bryce was just about to tell her, when her phone rang. Worrying it might be Chuck, she grabbed it. Unfortunately, it was Director Graham. "Agent Walker," she said as she put the phone on speaker so that Bryce could hear it.

"Walker. We have a problem," Graham said. "Bartowski has disappeared. We need you back in Los Angeles. You and Casey need to find him."

Sarah's chest tightened. "Do we know who's captured him? Who we're after?"

Graham's next words chilled her to the bone. "No. We think he's decided not to work for his government anymore. He's now a threat." She and Bryce locked eyes.

"What are my orders, then?" she asked, knowing what he was going to say.

"Retrieve the Intersect. If that's not possible, eliminate the threat," Graham replied. "There's a flight waiting for you at Andrews Air Force base."

As Graham ended the call, Sarah looked at Bryce. "So, you were planning on protecting Chuck again?" she asked.

Bryce winced. "Look. I couldn't talk to him about it, so I needed to make sure he was safe. My plan was to help him get away."

"But he beat you to it," she said, proud of Chuck.

He nodded. "It certainly seems that way."

"So, you want to hunt him down together?" she asked. "You think he'll trust either of us? Especially if we're together?"

"He's got strong feelings for you, hasn't he?" Bryce asked, rather than answering the questions.

She nodded. "And I know he hates that we were together before."

"We could be together again," Bryce suggested. That got him a glare. He held up his hands. "Okay, I know that's not happening because of your feelings for Chuck…"

Sarah sighed. He knew her too well to deny it. "I'm compromised to hell and back, but I don't think anyone could protect him as well as me."

Bryce nodded. "I think you're right, but he left when you weren't there to do that. Having said that, I suspect he found out about the new Intersect somehow. Would he have trusted you if you were there?"

That question had been playing on Sarah's mind since Bryce had mentioned the kill order. She'd like to think Chuck knew she would never hurt him, but was she right? Her shoulders slumped. "I don't know."

"Have you told him how you feel about him?" Bryce asked.

She shook her head, sadly. "How could I? Chuck can't keep secrets. Casey would know. I'd be sent away faster than either of us could blink."

"So, he just sees you following orders."

She nodded. She realized her eyes were starting to feel watery and had to look away.

"Maybe he'll trust me more, then," Bryce said, thinking that was a good thing.

Sarah felt even more miserable on hearing that. "Trusting his nemesis more than his protector," she muttered, and a tear did escape.

Bryce obviously noticed. He wasn't good with emotions, so he looked away. "We'll find him, Sarah. We have until then to work out how to play it."

She nodded. One thought cut through her misery. Be safe, Chuck!

Bryce spoke. "See you in LA." He handed her a burner. "I'll call you." Sarah nodded silently.

As soon as Bryce left, Sarah sprang into action to collect the gear she needed. She wasn't going to be late for this flight.

Casey picked Sarah up on her arrival at the Los Angeles Air Force Base.

"How did he get away," she asked once they were in his Crown Vic.

Casey was angry about this. "He put fucking loops on the security recordings, all of them. I don't know how he managed that."

"He outsmarted us," Sarah concluded.

"Now we have a kill on sight order," he grumbled.

She looked at him sharply. "If he doesn't come willingly," she qualified.

He shook his head. "Not my orders."

"We've been protecting him for four months and now we're to kill him?" She hadn't realized her voice was raised until he looked at her sharply.

"Bartowski's run. He's a security risk," Casey stated.

She slumped down in the seat.

"It has to be done, Walker. I'll do it alone. I know you can't do it." She looked at him in surprise. "Come on. I know you're compromised. Have been since the deli girl stole him from you."

Sarah huffed. "You're right. I can't kill him…. If we can capture him, will you spare him?"

He pulled over and stopped the car. "Walker, there's a new Intersect being made. When it comes online, he's to be killed anyway."

"How do you know?" she asked.

"Beckman has told me to terminate him then," He admitted.

This matched what Bryce had told her. "When did she order this?"

"Back in December. It's just a matter of time."

"I knew nothing of this," she said in a small voice.

"Graham and Beckman have known for some time that you're compromised," he said.

"So why am I involved now?" she asked.

"Probably because they think we have a better chance of catching him together," he replied.

"Are you okay with killing him?" she asked.

"I don't want to, but you know I always follow orders," he replied, looking unhappy about it.

"What if we save him? Keep him safe somehow?" She said that in a speculative way, even though she was actually planning on doing it.

He looked shocked. "You'd be going rogue. You'd be hunted down and killed, along with him."

"Hey, I was just speculating. I couldn't do it on my own. It'd have to be both of us, if we did."

"Never going to happen," Casey replied, his jaw tightening.

Sarah sighed. "I know."

Then, he said something that surprised her. "Of course, I wouldn't know if you went off and did it on your own. I would have to deny it if asked about it."

She gawped at him. "Really?"

"We'd be out separately, but coordinating the search," he replied.

"Really?" she repeated.

Casey sighed. "We had a rocky start, but you've been my best partner and he's been part of the great team, too. I know if he gets killed, you'll be ruined. I can't do that to you. Either of you."

She felt almost teary at those words. "Thank you, John."

Casey shrugged. "First, we should sit down and check to see if he's been picked up on any traffic cameras."

"You think he'd be that naïve after what he did at the apartment complex?" Sarah questioned.

"It's hard to hide from them all of them," he replied. "Get what you want, then come over to my apartment." He paused. "If we don't find him, I'll head in a northward direction. You go south," he replied.

Casey dropped Sarah at Maison23. She was going to pick up some things before setting off in her Porsche. Checking both phones, Sarah found no messages from either Graham or Bryce.

She called Graham, told him she'd arrived and she and Casey would be covering the ground separately to increase coverage.

"Good plan, Agent Walker," he replied.

"Any updates?" she asked.

"Nothing. It's as if he just disappeared."

That was good news and bad. Good that Chuck was not captured or killed, but bad that she had no leads on where he might be. "I'm sure we'll find him, sir."

"Remember. If he resists, shoot to kill."

She hated hearing that. "If he resists," she repeated.

Chuck's taxi ride had taken him to an urban area in south LA. He'd walked two miles, avoiding any cameras, which had been pretty easy. In this area, they were few and far between. He'd managed to catch a bus to a remote town, where he'd managed to buy a cheap second hand car at a virtual giveaway cash price in the early hours.

"Glad you can take it off my hands," the old guy had said.

Chuck had driven a hundred miles before finding a motel to stop at. The Wi-Fi was weak, but he managed to trace his journey. There was only one camera that had caught him, catching the bus. That camera 'developed' a fault, seemingly early that morning, so all recordings were lost. He'd been careful to avoid being caught on any street cameras while driving, but also checked security cameras along the route. One gas station had caught him, but that had 'developed' a fault five hours before that and nothing would show. It was possible that someone could track him via the 'faulty' cameras, but he had to take a chance on that.

Chuck opened his backpack and took out the things he needed. Hair dye, fake tattoo and all black clothing.

He'd decided to change his appearance away from home, not wanting to leave any evidence behind. Half an hour later, a goth guy with black hair and a large black tattoo on his cheek looked back at Chuck. The black hair extensions added to the change. Lastly, Chuck took a photo of himself so he could ensure the appearance was repeatable.

Then, he finally sat to check on Sarah and Casey, and their phones.

Casey's call from Beckman was as he had expected. He'd been the one who discovered Chuck had gone, but that hadn't been until the following morning when he'd bumped into Ellie and asked if Chuck was still in bed at ten in the morning. When he found out that Chuck wasn't there, he'd checked the security cameras and realized what Chuck had done. His call to Beckman was chilling. "The moron hacked into the security feed somehow. He's gone!"

Beckman asked. "Are you sure it was him? Or did some outside agency take him?"

"I don't know, General."

"Either way, he's now a security risk. Terminate him," she replied.

"Are you sure, General?" Casey asked. "I might be able to just bring him back."

"You were going to terminate him when the new Intersects were active. Just doing it sooner."

She paused and then said, "Or are you as compromised as Agent Walker?"

"No, Ma'am," he snappily replied. "I follow orders."

"Good. Do it, and do it quickly. Graham is sending Agent Walker back. I don't trust her."

He replied, "She always follows orders."

"Neither Graham nor I are sure of that with this one. She's being told to shoot if he resists, otherwise to capture. If she does that, you still terminate him."

"Yes, General."

Chuck hated hearing the certainty in Casey's voice.

He then listened to the call Sarah received from Director Graham.

He wasn't surprised at Sarah being called back to Los Angeles by Graham. He noted the pauses in her responses. He was sure that she was struggling with what she was being ordered to do, but she agreed to everything. Unlike what Beckman had said to Casey, Graham ordered her to capture and bring back Chuck and that only if he resisted should she shoot to kill. Sarah was the cool agent that he often saw, but the pauses in her responses were noticeable to her asset. What he didn't know was what that meant for him.

Was Sarah accepting her orders, like she usually did, and would kill him if he evaded capture? Or was she just giving the responses Graham wanted, with no intention of killing him? He didn't think she would kill him, but wasn't going to put that to the test.

Chuck wished that he'd been more confident when they were together. He wished that he'd kissed her as fiercely as she'd kissed him in that warehouse. Maybe even admit his feelings for her. However, now he was thinking more clearly, he knew she'd use that against him and entrap him.

No. The clear break was the right thing to do, in spite of how much it hurt.

A/N: As mentioned at the start, I know this sort of story has been written before, but I thought Bryce getting involved as he does here would be a bit different.

Whether you like this or not, please consider leaving a review. It'll help me know whether it's being read or not, in the absence of stats from Fanfiction, but I'd also love to read your thoughts about how this has started and what you think is going to happen.