A/N: Sorry for the delay, real life got in the way.

I want to thank everyone for taking the time to comment and feedback, glad you're enjoying this crazy idea in my head. Also, I didn't realize how short some of these chapters were until beta and some of the comments pointed it out, I will try to give you more per chapter going forward.

Thanks, Steelejay for all the beta help, as well as the idea's, it has been a big help.

I don't own Chuck

Black Rock – Barstow, CA April 20, 2009 – 11:30pm

Sarah and Casey had arrived and taken over command of the scene from the FBI. They very quickly realized that it was in fact a Fulcrum base; Chuck had been right. The computers had been wiped, although based on the equipment, there was no doubt Fulcrum had had Orion here to build them their own intersect.

Ted Roark's body was being taken away, his right eye gone from a single bullet wound to the head. The most noticeable thing was Orion was nowhere to be seen. Could he have done this? Was there a new group that took him?

Casey asked the FBI Special Operations team lead, "What led you guys here?"

"We got an anonymous tip about an imminent terrorist threat, so we geared up and came down. The strange thing is, when we got here, the threat had already been neutralized. We had over 30 prisoners either tranqed, unconscious or tied up. Quite a few of them needed medical attention, and it looked like they picked a fight with someone better. Must have been a good size team to take control. Only one fatality, that of Mr. Roark. None of these guys are talking and as you've seen, the computer and surveillance systems have been wiped clean."

Sarah was looking around, trying to comprehend what happened and how. The evidence techs were working to see what they could get, while the computer forensics teams were also doing their best. Sarah's thoughts drifted back to Chuck. As he was falling unconscious, he had mentioned this location. He knew, and she didn't listen. Instead of following her instincts or more importantly her heart, she had followed orders. She knew she had made the wrong decision, now she was just hoping with all her heart that she might get a chance to make it right.

She realized Casey was talking to her, bringing her out of her thoughts. "Techs are saying they believe there was an intersect cube here, but it's missing".

That was cause for concern. If the intersect cube was missing, along with Orion who had them?

As they made their way upstairs to discuss all the new information and call the general, one of the evidence technicians commented they had found a pickup truck from the airport. This was strange because none of the prisoners had ties to the Barstow airport. It wasn't much to go on, but Casey and Sarah thought it was worth the 15-minute car ride to check it out. They knew Roark had multiple private planes, and probably had access to plenty more that they didn't. Maybe they could find some new leads at the airport.

As they got to the Barstow airport, Casey drove in the gate but there wasn't much to see, being a small private airfield. There was a tower, only in use part time, several small twin engine and single engine planes, a couple of hangars, and then Sarah saw something that definitely didn't belong. A plain white G650, much like what the CIA, DIA, and NSA use to transport personnel and assets covertly.

"Casey, look over there, at your 2 o'clock, doesn't that look like a plane the NSA may use to say, transport a prisoner or asset".

Casey spotted the plane and immediately knew what Walker was thinking, the missing jet that had Bartowski on it. Maybe it didn't crash, but what was it doing in Barstow? Thinking back to their discussion with the General, was someone on the plane Fulcrum? The coincidences were starting to stack up.

"Let's check it out."

Casey and Sarah both approached the plane, guns drawn, though there didn't appear to be any movement. Casey pushed on the door handle and moved it to the open position. As he brought the stairs down, Sarah burst through with her gun drawn. They found 7 people all unconscious, all zip tied on the floor except one woman, who was reclining in a captain's chair with a blanket draped over her. Sarah went through and checked to confirm that everyone was alive. She was able to quickly confirm that they had all been tranqed, seeing the tranq darts still sticking out of most of them.

Working from the assumption that this was the plane Chuck had been on, based on when it must have left, they most likely had only been unconscious for a couple of hours at most. They would need the reversal drug to wake them up, so Casey called for support and medical.

While they waited for support, they started to check the plane. They quickly discovered that the gun locker was empty, and all the weapons the 3 NSA agents were carrying were missing. They would need to get a full inventory of what was missing from the agents and the flight manifest on file, as there was no manifest left on the plane. In inspecting the cockpit, they found the transponder had been turned off. That, combined with the gurney, IV and medical equipment in the back, served as further confirmation that this had to be the plane that Chuck had been on.

Once they completed their search, Sarah and Casey were trying to piece together what exactly happened. They were relieved that their worst fears had not been realized, since the plane had not crashed, but what happened? Who had taken out an entire plane full of experienced NSA agents? Chuck was obviously missing, as was along with Orion and an intersect cube.

Sarah was afraid that someone on the plane had taken Chuck and Orion, but they couldn't have been Fulcrum because why kill Roark and take out the base? Was it a rogue operation within Fulcrum? Too many questions, not enough answers. While Sarah was thinking about this, the backup and medical teams arrived, they would have their answers soon.

Barstow Airport – April 21, 2009 – 3:45 am

Sarah and Casey were standing in an empty hangar at the Barstow airport, it had been set up as a temporary staging error, taking care of the plane's crew, medical, and the NSA agents that were injured, a couple of which would require extensive PT, if not surgery.

They had spoken to everyone on the plane twice, going over the series of events twice each time. The stories were the same each time. The only one missing from the flight that took off was the asset. The NSA agents were especially angry that they had not been made aware how dangerous the asset they were extracting was Taking one look at him and thought he was some type of computer geek. Sarah couldn't help but correct them, "he prefers the term Nerd".

The most compelling interrogation was with the flight nurse, Melissa.

"So, you're saying that the asset woke up, and took out the doctor, 3 armed NSA agents, and both pilots?" Casey repeated for what had to be the 4th time.

"Yes" – Melissa stated.

"When he took out the pilots, who flew and landed the plane?"

"Chuck did" she answered for the 4th time.

Sarah finally interjected, "Melissa, what would you say if I told you that Chuck didn't have any combat or flight training".

"He may not have had training, but everything I have told you, and everyone else here has told you is true.

We were about to give him more sedative when he grabbed the doctors hand and bent it back, breaking it easily, you can't do that without knowledge or training. He then literally jumped off the seat and took out the 3 agents in 20 seconds, I have never seen anyone move so quickly. My boyfriend teaches martial arts, and his form and the preciseness of his strikes was unbelievable, no wasted motion.

After the guards were out, he grabbed one of their tranq guns, and tranqed them to be safe. Then he went to the cockpit. A short time later he dragged both pilots out and had me zip tie everyone. He helped me set the broken bones of the NSA agents and the doctor. He kept apologizing for hurting them, but said he had no choice".

"Why didn't he zip tie you or subdue you?" Casey asked.

"I wasn't a threat to him; I didn't know what was going on".

"Did you talk?" Asked Sarah.

"Yes, he had quite a story. He really seems like a good guy. He told me he was working on a team, and they betrayed him to General Beckman, all he wanted to do was try to save his father. To be honest, what he told makes me want to leave the NSA. I know he was some kind of asset; I've transported assets before, but not like him. He was genuinely a nice guy, said all he wanted to do was help. He also said General Beckman had already issued a termination order on him once. If everything he said was true, that and the bunker are illegal orders. We are not supposed to do that to good people.

When he was telling me the story about what had happened and why he was here, he was emotional, he didn't seem like any type of spy I have met before, he was really surprised that his team turned on him, he was hurt, deeply.

He also kept apologizing for all the trouble he had caused, he was going to try to save his dad, and if he survived, he said he would be on the run the rest of his life. I wished him luck and he did the same. Then he tranqed me and I didn't come too until the medics used the reversal agent."

"He is a good guy, your right about that" Sarah said.

Melissa looked at both her and Casey hard for a minute, then she realized "you were his team." She said more as a statement than a question.

The looks on both Casey and Sarah's faces confirmed what she thought.

Melissa looked back somewhat disgusted. "I understand following orders, but orders you knew were illegal. How could you? He was your teammate."

When no answer came, she left them with a final shot, "this is why we hate fucking spies, you have an impossible job, I get that. You deal with the worst of the worst, but when you turn on a teammate, a genuine good guy, I don't know how you live with that.

I hope he saved his dad, and I hope you never find him. I don't know where he learned to fly the plane or fight like he did, but what I have told you is all true. He's a force, and I wouldn't want to get in his way".

With that she got up and left the hangar to go to the motel they had booked for the agents and staff to get some rest.