A/N:

I Do not own Chuck

Chapter 6

Casa Bartowski – April 20, 2009 – 9:30 pm

Ellie Bartowski was on the verge of a nervous breakdown and her mind was racing a million miles an hour. Her father was gone and now her brother seemed to be missing, as no one had heard from him in hours, which was very unlike Chuck. She felt like she was missing something, and with her wedding just a couple of days away, she didn't know what to do. As she was trying to keep busy she got a text message on her phone which was strange.

"Go to your car" – CIB

Those were Chuck's initials, but why did she need to go to her car? She was angry that he had been out of touch and not returning her calls, so she went to her car, determined to give her a piece of her mind.

Ellie got to her car but no Chuck, just then her phone rang with an unknown number.

"Hello?" she answered.

"El, hi."

"Chuck, where have you been? Do you know how worried."

'Chuck interrupted her before she could continue the rant she had prepared for him. "Ellie STOP! I don't have much time and a lot to tell you. I am ok, I have dad and he is ok, but we won't be able to come to your wedding."

'"Chuck, what are you talking about? What do you mean you're not coming to my wedding, of course you are."

"Ellie, what I am going to tell you is going to sound unbelievable but it's all true." Chuck proceeded to tell Ellie the entire story as quickly as possible, the intersect that their father created, Bryce sending it to him, Sarah and Casey, and the fact the government had ordered his termination, and now the bunker. Chuck explained if he came back they would take him and hold him and he would probably never get out alive.

"But Chuck, they can't do that, that's illegal, they wouldn't do that."

Steven spoke up, "Oh yes Eleanor, they can, and they will. The only thing we can do right now is run."

"What about Sarah Chuck, she cares about you., I see the way she looks at you, she wouldn't let them do that to you," Ellie pleaded.

"Ellie, Sarah was the one who led me into a trap to tranq me so they could take me, and I couldn't fight back. Sarah Walker is the best CIA agent there is, and she follows orders. No matter how much I wish what we had was real, her actions just confirmed my worst fears. You can't trust her."

That information hit Ellie like a punch to the gut. She really liked Sarah and really did consider her one of her best friends. She thought she was perfect for her little brother and they were supposed to eventually be sisters. Now she was hearing that it was all fake, all a 'cover.' The combination of hurt and anger that flared through her took her breath away. Not only that, but the fact this was going to keep her father and more importantly her brother out of her wedding and her life for an unknown amount of time, and Ellie Bartowski was beyond angry.

"So what do I do?" she finally asked.

"El, it's up to you, but I could never ask you to delay getting married to Devon. I'm sorry I can't be there, but you should definitely keep your plans and marry Devon."

Ellie heard what her brother said, and while she was still trying to process it. Chuck was right, she didn't want to wait any longer to marry Devon, as desperately as she wanted her family to be there, she wanted to marry Devon more.

"Ok Chuck. I want you and dad there, but if you can't be there, I am going to marry Devon."

Chuck was glad his sister would go through with the wedding, she was going to need Devon.

"That's great El, will be thinking of you and watching in our own way.

There is something else you need to know, you know the research you have been working on with Dr. Kirk?"

Ellie was surprised, she had never mentioned Dr Kirk or the research he had asked for her input on, the theory was all hypothetical.

"El, dad is Dr Kirk. The research you have been doing has been helping me with his Intersect updates."

"WHAT?"

Ellie was stunned, this was all too real, and it was in her brother's head.

"El, you can't tell anyone about this, and you can't talk in the apartment. It's bugged with cameras and listening devices courtesy of the NSA. The good news is, the computer dad/Dr Kirk sent you, you can use that to communicate with us, it's encrypted and can't be traced."

At this point, Chuck knew he needed to hang up. "El, we have to go. We'll be in touch as soon as we can. I will see you again, I promise. I Love you. Have a great wedding and know dad and I are there with you in spirit."

"'I love you too little brother. Please be safe. You too dad'

"Thanks, Eleanor, I love you too."

And with that they were gone.

Castle – April 20, 2009 – 10:30 pm

Sarah watched the video of Jill Roberts talking with Chuck, needing to know what Jill had said. When she heard Jill tell Chuck the NSA, CIA, and Fulcrum were all the same and used people, and he couldn't trust any of them, Sarah was heartbroken. She had been the one to prove that Jill was right. He couldn't trust them. She and Casey, the ones who had sworn to protect him, had betrayed his trust.

Sarah was really feeling it, she knew she made a mistake. Perhaps the worst in her life. She had to fix this, even if Chuck would never trust her, she was going to get him out of the bunker.

She was lost in thought when Casey yelled, "Walker, the General wants to talk to us. Now."

Jolted from her thoughts, she went into the main room and waited for the General to appear on the screen. She could feel that Casey was also having second thoughts about what they had done.

The screen came to life and the General appeared a bit haggard.

"Agent Walker, Major Casey. The plane that was carrying the asset from LA to the bunker went missing a few hours ago. We have no word, and it looks like the transponder stopped transmitting."

"What does that mean General?" Asked Sarah, knowing the possibilities were not good.

'"There are really only two possibilities; either the plane was hijacked, or it went down. We are checking to see if anyone on the extraction team might have been Fulcrum."

Sarah stood there, feeling a sense of dread, like ice water had been dumped down her back. She was numb. What had she done? If she had just gone with her instincts, her feelings, Chuck would be with her. They might be running from the US Government, but they would be together.

"What are our orders Ma'am?" Casey chimed in, knowing Sarah was going through emotional turmoil.

"While we searched for the plane, I received an alert that the FBI had been called to raid an underground facility in Barstow. It appears Ted Roark was found dead, and there were a lot of tranqed and tied up agents, we believe to be associated with Fulcrum. I want you to go and take command of the scene. Our latest intelligence suggested that Orion was supposed to be there. Find out what's going on and I will update you when I hear more about the search for the plane."

With that the screen went blank. Both Casey and Sarah looked at each other thinking.

The plane that Chuck was on is missing. A Fulcrum facility was hit, the same facility Chuck mentioned in falling unconscious., Ted Roark is dead, and Orion is missing.

Logic would seem to imply that this was Chuck's doing, but a few things didn't make sense. Chuck was tranqed with a heavy dose and should have been unconscious for hours. No one on the NSA extraction team would reverse this. Second, Ted Roark was dead? Chuck hated violence. Last, but certainly not least, Chuck didn't have the skills to pull off an operation of this magnitude.

They got their weapons, made their way to Casey's Crown Vic and were soon on their way to Barstow.

The car ride was quiet, both lost in their thoughts.

Finally, Sarah broke the silence. '"Casey did we do the right thing?"'