A/N: Doing 2 chapters this time, appreciate all the feedback, let me know what you like don't like. I am still working on this, and it has turned out much more than I expected, still not sure how I am going to end it, so appreciate any feedback.

I Do not own Chuck

Chapter 3

Gulfstream V taxing from LAX – April 20, 2009 – 7:30 pm

As the plain white G650 plane takes off from LAX an NSA doctor and nurse watch over their new charge. The doctor looks down at Chuck wondering what is so special about him. Looking up at one of the extraction team guards he asks "When do we arrive Davis-Monthan? I need to know at what levels we have to keep the sedative?"

"A little over an hour" the guard curtly replies. "Upon landing it will be about another 90 minutes to reach the secure location."

"Thank you" replies the doctor while raising his eyebrows to the nurse.

What none of the passenger on the plane realize is the governor in Chuck's watch are sending ever increasing electric shocks in small bursts to his body slowly waking him up from the effects of the sedative, and in only a matter of minutes Chuck will be awake.

25 minutes later Chuck is groggy but awake, his eyes still closed and his breathing slow, to appear he is still asleep. He is not restrained, and his mind and the intersect are forming its plan. Based on the voices he knows there are at least 4 people in the cabin, at least 2 guards and 2 medical staff. He figures there are 2 pilots maybe a 3rd or 4th guard. Then as he can sense the doctor preparing more sedative in a syringe.

Then it hit him, for the first time he flashed on it, he knew Kung Fu.

3 months earlier - January 15, 2009

Chuck was on his bed on a rare night off from missions or doing something to 'protect' the cover. He was reading a comic book, when his computer came to life. , he could see the web cam was active. He got up from his bed to see what was going on, while at the computer the following message came up

I know your secret.

Chuck, thinking one of his friends was playing a joke, 'haha, very funny. What secret would you be referring to?'

I know you're the Intersect.

Seeing that Chuck froze…'Who are you?'

I'm Orion…

'And who is Orion?' Chuck asked out loud with a mix of excitement and fear.

I created the Intersect.

Chuck sat there stunned and confused. 'Sorry, but I am not just going to take your word on this?'

The next moment a symbol appeared on the screen causing Chuck to flash, all of sudden all the Intersect files were running through his head, including a list of the team who worked on the Intersect, including one Stephen Bartowski.

'Dad?"

At this, for the first time in 15 years, Chuck Bartowski was looking at his father on the computer.

'Hello Charles, its good to see you.'

Chuck was dumbfounded, 'Dad, where have you been, how did you know I was the Intersect, can you get it out of my head' he stammered almost all at once.

Charles, I know you have a lot of questions, and are probably mad about a lot of things, and you have every right to be. Let me try and take this one at a time.

As I mentioned, I led the team that built the original intersect, I have been on the project in quite a while, but all the really cool stuff was me. How I know you're the intersect is, I have been hacked into the CIA, NSA, DIA, DNI systems since before I left you and your sister, there cyber security is really subpar. I needed to keep track of what was happening, and also keep them from finding me.

Where have I been? All over in a sense, I have been on the run from the CIA, they wanted to continue to use my research in ways I didn't want, so I left. Part of the reason I left you and your sister was to protect you. As you have seen, the government is not above using people for leverage, and by leaving they couldn't go after you and Eleanor.

'You left to protect Ellie and me?' Chuck was struggling trying to absorb what his father had just told him.

I never meant for you and your sister to be part of this, Bryce never should have sent you the damn intersect.

'You know Bryce?' How did his father, who he hadn't seen since he was 12 know his college roommate?

Yes, he was one of the agents I worked with. And he left it at that.

'Since you created it, does that mean you know how to get the intersect out of my head?' Chuck asked excitedly.

Not yet, but I have an idea that I think will work. Unfortunately, it will take me some time to work things out before we can try it. Not having and Intersect computer or the intersect Cube will make it take longer, but I am confident we can make that happen.

'That's great, I can't wait to tell Sarah.' Chuck said excitedly, like a child at Christmas.

Charles you can't tell anyone until the Intersect is out of your head. You can't trust them.

Chuck was shocked, he trusted both Casey, but especially Sarah with his life. They became a good team and he trusted them implicitly, not just with his life, but especially Ellie's.

'What do you mean dad, there my team, and we're friends. They know how bad I want this out of my head, they'll be happy for me.'

They are agents Charles, and they will need to report this to Beckman, she is someone you absolutely cannot trust. You are her ace in hole in the fight with Fulcrum, she will not want you to have the intersect removed. You cannot tell anyone about our talk.

'Dad, they probably already know, the entire apartment is bugged with both audio and visual surveillance. They are probably trying to trace you IP now'.

I took care of the surveillance; both have been looped for the last 20 minutes showing you reading your comics on your bed.

Chuck smirked, of course he had taken care of it. He was eccentric, but he was also brilliant.

I left you a present Charles, in your top right desk drawer.

Chuck opened the drawer to find a box, inside was a pair of sunglasses, much like the one Bryce had left just a month before with the Intersect update, as well as 2 watches. One looked like the watch Sarah had gave him for tracking, the other was nicer gold banded, something you would wear to a more formal event.

'Are these intersect glasses dad? And I already have a watched courtesy of the NSA'.

Yes Charles, those are intersect glasses. I know you recently got an update via similar glasses from Bryce. I wanted to give you some more protection, so I have given you an update, but it is more than informational, these updates will include skills, languages, more spy like skills, so you can better protect yourself.

'Dad, why would you give me an update with spy skills if we're going to remove it?'

Charles, as I said, I have an idea but it will take time. This update includes self-defense, weapons training, piloting, dancing, foreign languages. Basically, you become Jason Bourne without needing the years of training. This way, if Beckman places another termination order on you, or the tries to take you to a bunker, you can fight and escape, and learn to live in the shadows until we are able to get the intersect out.

'I can't wait to tell Sarah, now I won't be yelled at as much for not staying in the car'.

Charles, they can't know you have these skills or abilities. You need to keep this quiet and only use them in life and death situations.

'What are the watches for?"

They are what I call the governor. They help to balance your neurol network, with the intersect, because of all the current in your body when flashing, eventual could lead to issues with your brain, these keeps those levels in check, and you will be able to live as you normally do. I created one to replace the NSA watch, complete with the same tracking chip and number, so they won't even know you swapped them.

Another improvement I have been working on is making the flash smoother. You shouldn't have pain or discomfort, and you should be able to hide the flash, so other people will not notice. You will still be vulnerable for a few seconds during the flash, but otherwise it should be like you're remembering something. Over time, the skills and languages should imprint in your mind, so even if you no longer have the intersect, you will still have the knowledge and be able to do the skill as if you had spent years learning. Ultimately, that's what I wanted the intersect to be a teaching tool.

'Dad, that's amazing. How did you come up with the idea, and how did you accomplish it?'

I worked with neurologists, I created the intersect for the mind, thinking liking it's a computer. But after a lot of trial and error, there are distinct differences between the way the mind holds information and a computer. Your sister was actually one of the key neurologists who figured a lot of this out.

'WAIT, you worked with Ellie? She didn't say a word, why wouldn't she tell me?'

We never met or talked on the phone; it was all over email. She thought she was helping on a theoretical idea. She has no idea that anyone, let alone you have a computer in your head.

'So, what happens now? I take the update then you eventually remove the intersect. With these changes, I could help a lot of people' Chuck said thinking it would be kind of cool to finally be able to protect himself.

Charles, its up to you. I hope you take the update; I would feel better knowing you could flash. It also will help, as you would have more information and be better prepared for missions. I wouldn't tell anyone, if Beckman finds out, she will want to turn you into an assassin, and more than likely take away your handlers.

Chuck realizes his dad is right, Beckman would try to turn him into what Sarah and Casey used to be. He couldn't imagine not being part of this team. But his dad brought up good points, it would be better to take the update to protect him, Ellie. Even Sarah and Casey. He just couldn't tell them.

After a moment to think about it, Chuck put the glasses on and the update began. This felt different than the original upload and even the update from Bryce. Like his father mentioned this was smoother. It was over quickly, and he almost felt refreshed. He replaced his NSA watch with one of the governors, and it was like a weight had been lifted off his head.

Ok Charles, how do you feel?

Better, lighter.

Another improvement here is you don't need external stimuli to flash, if you think of how to fly a plane, you will flash on how to fly a plane. If you think about needing to know how to do Kung fu, or how to speak Russian, you will flash on those skills. If you are looking for information on someone, if its in the intersect, you will flash on them. I tried to make it more, user friendly.

'Dad, how do I explain that to Sarah and Casey, that I can search the information in my head?"

I would not tell them about the skills, but I would just tell them after almost 2 years, you have learned there are ways to search that you didn't realize before.

Charles, I need to go. I am watching, if you need anything, just think, and you will know how to contact me through the intersect. I can't stress, you cannot tell anyone we've spoken or the updates. You cannot trust them.

I won't dad.

Practice with the intersect, get used to looking for things in your mind. That way if you have to use the skills, it will not have been the first time. You are good enough hacker, so just be sure to loop the surveillance feeds before practicing.

Thanks Dad, I will. Be safe.

You too son, we'll talk again.