A/N: Hey everyone. Sorry it's been so long. A large variety of reasons as to why it's taking longer to send new chapters. I would like to get to chapter 20 by end of June. But we will see if I can hammer out a couple more chapters. Thank you all for your support. Don't forget to review!

I don't own Chuck or anything remotely famous

Chuck vs the Antithesis

The team packed up and headed out to the 5th location that they had found in 2 months. They flew through the facility. Meeting very little opposition. But they did find a server that Chuck was able to get on and take some information.

They did take down and capture several lower level Ring operatives, but most of them had a cyanide tablet in their mouth. Killing then once they bit into it.

They had struggled to find this one lead, and now they felt they had nothing. This was a dead end as far as they could tell. With a huff, they made to leave.

Shaw watched them exit the facility. "I thought you said that he was incompetent." A distorted voice on the other end of the phone call said accusingly. "He is. He just gets lucky from time to time." Shaw responded defensively. "His luck had better be running out, and quickly. Or there will be consequences." The voice said, as the call ended.

Shaw continued to watch the recording. They were getting closer than he expected, and that was unacceptable.

Chuck flopped down onto his bed. He hasn't felt this defeated in a while. He was running out of ideas on where to go from here. He was just starting his downward spiral of self deprecation, when there was a knock at the door.

Dragging himself out of bed, he made his way towards it. Opening the door, he was immediately pushed out of the way by an already talking Morgan. "Why do I now have a key already man? I get you have this super secret life of Spy-atude, but it's ME man! And this entire not spending time with me for months on end crap? That's coming to an end. I'm not asking to be a part of them team, unless you are looking? No. Ok, yeah. I'm not even asking for a spot. Just need me my Chuck time. Now, I have some grape sodas, some pizza, some Sizzling Shrimp, and both the new. Call of Duty AND the entire Star Wars saga. All 6 movies. On Blu-ray. Oh yeah. Oh and the new Star Trek movie. If we feel a bit nasty."

Chuck just stood there and smiled. He had missed his best friend more than he had realized. The toll of the life he was leading really was more than he could handle at times. It was always nice to have a reminder that to some people he wasn't a spy. Or a big name hacker. He was just Chuck. And that's all they expected of him.

"Yeah buddy, I'll have to get you that key soon. And I think I'm feeling pizza and Star Wars tonight. Not in a gaming mood." Chuck said with a slight shrug.

"Say no more my man! One Star Wars Marathon coming right up!" Morgan says as he starts to set out the food on the coffee table.

The movies start, and the friends talk like old times. Chuck tells him about his dad dying, and that it happened on mission so he couldn't tell him. Morgan came and sat next to him and gave him a hug. They proceeded to sit and reminisce about what his dad was like when they were kids, while the movie played in the background.

"You remember after we watched War Games, and your dad thought us how to Demon Dial?" Morgan said with a laugh. "That was one of the craziest things I ever did. But that seemed to jump start your craving for hacking. It was crazy." Morgan shook his head with a smile at his friend. "He always had some secret to share with us. And usually there was more to it. Some hidden.."

Chuck's mind trailed off. He started thinking, Dad always left more than what was first seen. He always gave extra that you had to work for.

"Chuck, you ok?" Morgan said, shaking his shoulder. He had a concerned look on his face.

"Morgan, you may be a genius!" Chuck proclaimed as he shot up out of his seat and took off towards his lab.

"Well, obviously… wait. Why? What I say?" Morgan followed Chuck, and walking into his lab he stopped. He knew Chuck worked for the government now, but he had never considered what that might mean exactly. Chuck's lab made the work area at the BuyMore look like a trash pile. "Woah.." he murmured, as he slowly looked around. Seeing multiple computers, he knew which was for gaming. He'd known his friend far too long to not.

"You reminded me that my father was notorious for leaving hidden clues and messages our entire life. Little things that not everyone would know or pick up. And that made me think of our current mission status, and how my father may have left more for me than I saw originally." Chuck stated excitedly as he typed away on his laptop.

"Oh. Yeah. Of course! Happy to help." Morgan said, still awe struck by the lab. He gradually worked back to where Chuck was working, and as he did he looked over chuck's shoulder.

Chuck knew that Morgan probably shouldn't be seeing what he was doing, but he didn't want to waste time. Typing away, he finally found it. Pulling up the file, he found it was password encrypted. Great. He flopped his hands down onto the desk feeling a bit frustrated.

"You said your dad sent this to you. Right?" Morgan asked.

"Yeah. He did." Chuck said dejectedly. He knew that if his dad had encrypted it, he wasn't getting it open without the password. No one was.

"Well. Just me thinking, but wouldn't it make sense that it would be something he knew you would know then? Like. Not over complicate it, but make it something you and him would have a connection on?" Morgan said again, trailing off at the end as he clearly wasn't sure of himself.

"That.. actually makes sense." Chuck said, again a bit surprised that Morgan was actually being this helpful.

"I have my moments. Just don't let Big Mike know, he will expect more from me!" Morgan said as he let out a shudder.

"Don't worry buddy. Your secret is safe with me." Chuck said with a laugh. He started typing in things he could think of. After a few attempts he runs his hands through his hair and sits back. His eyes land on the Tron poster. And it clicks. He types in

/HE FIGHTS FOR THE USERS:

Suddenly the Orion symbol comes on screen. And, after a brief loading screen, a video of his father appears.

"Hello Charles. I knew you would find this, and hopefully sooner than later. These files will contain information that will be dire to what you and your team are doing. But be warned. There is no way to undo opening some of them. The owners will be notified, and they will be coming after you. There isn't anything I can do to stop it. Especially now.

I do want you to know, I had been in contact with your sister the last few weeks. Even though she does not know it was me. I was monitoring her progress with the Intersect, as well as your own. I'm very impressed with how far you have been able to take it. I am very proud. I have a patch for you, that I believe will help you greatly in what you're trying to accomplish. Hit enter and esc at the main screen with the files and it will activate.

Please know I never meant any of this for you and your sister. I wanted a better life for you. One away from the spy world. But it has found you and her anyway. And since that has happened, you will get access to the rest of my files as well. Our old house has them, and you will find instructions among these files as to how to find them.

Remember, you are special in a way that no one else could be. I am sending this before I breach a building that could be very heavily guarded, and I hope you won't see this. But if you do, know I always have and always will love both you and Eleanor with all my heart."

And the video cut out, and a folder with multiple files pops up.

"What does he mean by a patch?" Morgan asked, startling Chuck who had honestly forgotten his friend was there still.

"He is talking about the Intersect. The program that I downloaded into my head. The reason I am working for the government in the first place." Chuck answered. He still wasn't sure if he was going to put the patch in or not. Probably should talk to Sarah about it first. And maybe Beckman. Chuck thought as he started to look at the files.

"Morgan, I know we said that this was a guys night, but is it ok if I call Sarah?" Chuck said hesitantly. He knew he hadn't gotten much time with his bearded friend lately.

"Dude, it's no problem. This is kind of a bigger deal." Morgan said, still sounding a bit stunned from the amount of information he is having to accept at this point.

Chuck had a brief conversation with Sarah, and then called General Beckman. Both cautioned downloading the patch without Ellie taking a look at it first. Which he agreed. So, instead, he worked on the files. He figured out which ones were going to be the dangerous ones to open. And he figured out the basics of why.

A few days later he called for a team meeting. He had explained everything to Ellie, and she was on board with the patch as long and she could be there to monitor. And Chuck had everything ready to tell the team what he had found. He forwarded everything to his private server at Castle.

They all met in the conference room, with Chuck hooked up and being monitored in the side room. The patch was designed to help him process physical information and help his mind control his movements and breathing. It was specifically designed to match Chuck's current brain wave activity, something Chuck and Ellie had been working on with the original design.

"Chuck, are you ready?" Ellie asked, glancing at the monitor displaying his brain activity.

"Yeah I think so. It's not like this is ever comfortable." Chuck replied with a slight nervous laugh.

"We will be right here this time." Sarah said comfortingly. Which made Chuck smile.

"Ok. Here we go." Ellie said as she hit the buttons and the screen in front of Chuck came to life.

The flashing went on for a while, and one it was done Chuck slumped in his chair and the screens went dark again.

"His vitals all remained normal. That's weird. He didn't even have his brain heat up this time, but the monitor showed his entire brain was lit up like the 4th of July. It doesn't make sense with how he was in the past." Ellie said, clearly very confused. "This will be something I will have to monitor."

Sarah had already left and rushed into the room Chuck was in to check on him. She heard Ellie say that his vitals showed he was perfectly ok, but he had passed out. And Sarah didn't like that. She rushed up to him and unstrapped him from the chair. "Chuck. I'm here. Are you ok? Talk to me Chuck."

"I need to get my presentation ready." Chuck mumbled, still half out of it. His eyes still closed.

"You just sit here for a moment and recover." Sarah said, as she climbed into his lap.

"You sitting in my lap is going to recover something, but it won't lead to me resting any." Chuck said with an edge to his voice. Causing a giggle to erupt from her chest.

"Ahem. I hope I am not interrupting anything. But we are waiting for Chuck to tell us why he has requested all of us to be here. If he has a moment free?" A somewhat irritated sounding General appeared on the screen in front of them.

Quickly jumping off of Chuck, Sarah said, "Yes General." And marched out of the room, leaving Chuck staring at the General. He couldn't help but grin a bit. Which caused Beckman to shake her head and close the video feed before she smiled herself and betray her stern persona.

Chuck walked into the main conference room, and pulled out his laptop. He started pulling up files, but being careful to not open any of them.

"Ok. I have a lot to get into. I'll need input and permission to continue with this research, once we do this there is no going back. I want to make sure that everyone knows what it will mean for us. For all of us. This isn't something to be taken lightly. It's an all or nothing decision too." Chuck paused to breathe and let everyone take in what he said.

"What are you getting at Bartowski?" Casey growled, not liking the little dance around the information that Chuck seemed to be doing.

"Ok, buckle up kids. We are going on a bit of an adventure." Chuck started as he started pulling up pictures, files, and slides. Filling the entire screen several times, as Casey groaned slightly. "So, this started the other night when Morgan was over and we were talking, he brought up the fact that my father always likes to hide extras in all his work. Really, in everything. He would make little games and riddles to solve to keep me interested and give my brain a workout before I was able to get the extra information. And he did similar with the video that he sent to me and Ellie." Chuck rushed out, trying to get through it all but realizing he was talking way too fast.

"Yes, you weren't the only one he liked to do that for." Beckman injected, "It just drove most of the rest of us nuts." She finished, causing everyone in the room to slightly chuckle in recollection of the man.

"So, the extra files and different information that he left for me this time is what you see in front of us." Chuck continued. "These files are the building blocks of a mix domestic terrorist group slash cabal." Chuck cycled through the documents slowly. They were able to read parts of them before he moved on to the next, only none of it was making sense.

"Talk nerd for brains." Casey growled, getting frustrated at the pace that Chuck seemed to be dragging this out. He respected the kid, but he didn't like the feeling of being left out.

"Ok Casey, settle down. In these documents, if you read through them all, you will find names, dates, financial records, etc. All relating back to several groups. Some of which we already know to be members of the Ring." Chuck stated, giving a brief pause to let the information sink in before he continued. "It would appear that Graham, while he was despicable, had come across this group and was treading carefully in his research. Which is quite smart since, as you can see, there are many fortune 500 companies listed among the members, as well as several Senators that are prominent in their parties. This group is far well embedded into our government, defense, and tech companies. You could almost make the claim that they are running the country, or would be with very few moves. However, a majority of the major players seem to be privately owned companies or financial groups that no one has heard of, but fund many campaigns and hold many government contracts." Chuck paused for a drink.

"So, you're saying that this could be something that could cripple the US if we were to actually take it out?" Sarah asked with clear hesitation and unease in her voice. What had I committed my life to serving? Was my actions ever about saving people? Protecting people? Serving the government? Or was I always a privately owned slave masquerading as a weapon? Sarah lamented internally.

"I am not sure. I know it will effect our country as a whole in some way, but I am not sure how deep the rabbit hole goes. Like Shaw had taunted, I didn't understand what I was getting into. But I think I am getting a grip on it. I also believe that I have found a listing of properties that they own. We would have to work off the record for most, if not all of this, as they would have people in place to be able to track us. I am sure that, especially after our interactions with Shaw, we are now on their radar like never before." Chuck warned slightly.

"I know that I am secure here, and I just need to know, are they after the Intersect or are they after Sarah? What is it that made them come after our team?" Beckman asked curtly. She was clearly uneased at this revelation.

"Simply put? Everything. They seem to want control of everything. They seem content to rule from the shadows. Pulling strings, and cutting strings as needed to get what they want. Achieve their goals, and then back into their private lives. Never allowing themselves to be in any kind of danger. But putting so many others in far more danger than they would choose on their own. They seemed to have learned the value of the shadows. Not wanting to be the face of anything. Recognizable but never known. All the power, with very little of the responsibility." Chuck finished as he continued to cycle through the files.

"They sound like real pieces of work." Casey said with a scowl plastered on his face. These were the exact people he never liked, and yet, like Sarah, he can't even tell if he had been serving them unwittingly or not for years. Given up more of his life than he would ever like to admit to, and for what? The security of some rich people's investments?

"It is good to know who you're fighting, and now we know." Beckman said, trying to sound positive. Even though she was even struggling to find the silver lining.

"I did find one thing that would be of a high benefit for us." Chuck said with a slight smirk.

"What is it Chuck?" Sarah asked, even she had a slight clip to her tone.

"I am pretty sure I found where Shaw is. And the specs for the compound." He stated, pulling up the location and information. Earning grunt number 11, excitement with the hope of gun play.

Landing in Colorado they made their way silently through the forest to the compound that Shaw was said to be in the documents. Approaching the wall they paused to discuss their strategy. Chuck had his laptop out, and was in their system. He was ready to shut down the entire plant as soon as they were ready, he just waited for word from Casey on when. Sarah sat, rechecking her ammo and knives to make sure she had all she needed.

Shaw watched on the surveillance monitors as the group approached. He had hoped they would be so bold as to find him. They had set off the silent sensors in the forest that had been set up to make sure they could keep an eye on anyone that was after the one true perfect Intersect. And now he would finally get the opportunity to take out the weaker form. Show once and for all who the real Intersect was. Bryce had been weak. Sending it to Chuck, when he was set to be able to take it for himself. Too scared to take that chance. That risk. But now it worked out for Shaw. He was now the perfect Intersect. The perfect Agent. The perfect killer. And no one would be able to stop him. Not even Sarah Walker. He had a plan. Now he was able to make it happen.

Chuck got the nod, and looped surveillance for them to make a silent entry. They didn't want the entire compound to know that they were there. Casey and Sarah took out the single guard that was on post with ease, and they made their way towards the main building.

"I know I shouldn't say this, but has this seemed easy to anyone else? Like, too easy?" Chuck asked hesitantly. Looking around, and seeing very few people.

"Yeah, I don't like it. Keep an eye out. I'm smelling a trap." Casey replied. Always the marine first, he was vigilant. Not wanting his team to be at risk.

Sarah stayed quiet. She didn't like this. It reminded her of too many missions that went south. And usually those were the ones that she had blank spots on. Times she didn't remember, but then would wake up later covered in blood. Even though she had minor injuries. The times that she didn't want to know. The times that she was scared of what would happen if Chuck saw her like that. When Chuck didn't see Sarah anymore. All that was left was the killer. She took a deep breath and cleared her mind. She had to focus. Everything else would be handled once they were no longer in danger. Well, immediate danger anyways.

Chuck hooked up his wrist computer to the doors security panel, getting through it with ease. Before he opened the door, he flashed on his martial arts skillset. That did nothing to help his fear. As soon as the trio was through the door, it shut and he heard it lock. Not good. He thought, as he looked back at the door. Suddenly, the alarm sounded. A trap. Of course. Chuck took off towards the security room so that he would be able to set up and find everything he needed. Sarah and Casey took off after him. But the training he had been doing with Sarah, along with the increased influence of the Intersect had been helping him. He was faster than them, his long legs eating up the floor faster and faster. And as he made yet another turn, they lost him. The dual doors shut behind him, and Sarah crashed into them. They were locked. She kicked the door in frustration. Blocked off from the man she loved.

Casey got on the coms. "Hey Bartowski, forget something? We are shut off from you. We will try to find another way through, but for now you're on your own."

Sarah put her hand up, stopping Casey. She heard boots approaching. "Casey, we have to get out of this corridor. We are truly trapped here. No cover at all." As she finished, the first of the troops came around the corner. There was nothing they could do. "Chuck, finish this." She said in her coms before setting her gun down and raising her hands in sync with Casey.

Chuck froze momentarily at hearing that they had been captured. But he knew that his best bet at getting to them would be getting set up in the security room. Where he would be able to get control of the complex. He hurried around the last few corners, approaching the room with hesitancy. After confirming that there was no trap on the door, he unlocked and opened it. Walking into the darkened room he hears, "Hello Chuck."

Shaw was standing in front of the monitors. "You really think you are that good of a hacker? That you could just walk into one of the most secure places on earth without any resistance? When are you going to learn your limits? Or that anything you can do, I can do better?" Shaw said with a smirk.

He hit a button on the keyboard by his left hand, and on the main screen it changed to show Sarah and Casey surrounded by military. "If you hurt them." Chuck started.

"You will what? Kill me? Please. Chuck. We both know that that just isn't in your nature. You aren't a killer. You apologize for running into chairs. To kill another person is just now in you. Now, me on the other hand. Did you enjoy the performance I put on last time?" Shaw said with a smirk. "Your father looked so helpless as he laid there. The look on his face was amazing when he finally realized he had been shot. But nothing will ever compare to the look on your face when it dawned on you what was happening. It is something that I will cherish for the rest of my life. Almost as much as when I finally rebreak Agent Walker and get her back to what she was made to be. A perfect, order obeying, robot. She was trained to not have weaknesses like emotions. The perfect woman. And this time, she will answer to me. You see, there is no way out for you. There is no where you can go. There is nothing you can do. And, as far as the government is concerned, you aren't here. So there is no back up coming. You have nothing. And there will be no record of this anywhere." Shaw ranted on, praising himself.

"So this isn't a military base? Those aren't US soldiers?" Chuck asked.

"You really are just so slow sometimes Chuck. Do you need everything spelled out for you? How did you even get into Stanford? It is no wonder why they kicked you out. No, those aren't military. They are in the Ring. They are provided by our generous benefactors. These men happen to be provided by Volkoff industries." Shaw scoffed at him.

Making sure that his com was active subtly, Chuck replied, "So, these guys are Russian?" Keeping the com active so Shaw could be heard.

Shaw replied, "Yes Chuck, and 2 2 = 4."

Chuck heard Casey give a disgusted grunt, and Sarah softly laugh at what she heard. They didn't have to hold back. They weren't hurting good American soldiers that were just following orders. That made this entire operation easier. And easier to report after the fact. Chuck tapped a couple keys on his wrist computer, and the lights turned off on the entire compound. The screens went black. And he lunged at Shaw.

Sarah and Casey waited for it. As soon as the lights went dark, Casey knocked the gun away from his back, and launched his head at the enemies. Breaking their nose and knocking them to the floor unconscious. Spinning as he kneeled, he kicks out and breaks the next guys knee. He grabs the first guys gun that he dropped as he spinned, and fires several rounds at where he remembered other guys being. The flash revealed them to no longer to be there. He pauses and hears only breathing. "Sarah?" He asks.

"Yeah Casey. We are clear." She replies calmly.

"Good. Let's go find Chuck." Casey says, as he gets up and starts making his way down the hallway. Thankful to have Sarah as his partner.

Shaw saw Chuck lunge at him, and moved out of the way. He activated the Intersect, and flashed on the martial arts skills. Smirking, he expected this to be easy. He knew that his Intersect had been upgraded, far from what Chuck had originally downloaded.

Chuck recognized Shaw's face as he flashed. He had left his coms on, so he let Sarah and Casey know, "Shaw, did you just flash?" Chuck asked.

Shaw didn't reply this time. He just smirked and came at him with a right jab at his jaw. Chuck dodged the jab, and then moved to block the left knee that followed. Shaw started out with a barrage of attacks, hoping to end the fight quickly. He landed several, but as the fight continued and he was unable to get Chuck down, Chuck seemed to be getting quicker.

Chuck felt the Intersect kick in, his patch that he had downloaded calming his mind. His emotions were still there, but in a dampened state. He felt calm, even as there was slight pain from the blows that Shaw had been able to land already.

Limbs were flying everywhere. Chuck was blocking more and more of Shaw's attacks. Left jab, right hook, left kick, left knee. It was all slowing down. He felt the Intersect reading it and it felt natural. Not like before, where he felt rushed. Not like with Sarah where he felt something was controlling his body. This felt like muscle memory. Like he was reacting, not a program running in his mind. He watched Shaw as arms and legs were being thrown.

Just then there was a ramming sound on the door. Chuck looked up to see Sarah and Casey looking through the security glass. It distracted him enough for Shaw to get a kick in. It landed square in Chuck's chest. Sending him flying back and slamming into a table. The wind knocked out of him, he staggered. He didn't realize how tired he was.

Looking up he saw Shaw was breathing heavily, but had a confident smirk on his face as he came at him. The look in his eye was of murder. He was ready to kill Chuck and end this. Chuck started glancing around the room. His mind running as fast as it ever had. He knew that he had to do something. That kick had been more than he expected.

Shaw ran the last few steps toward Chuck to gain his momentum, and then leapt at Chuck with his knee out in front. He is looking for a death blow.

Chuck grabs the mouse and keyboard off the desk on top of him and lays down on the floor. The knee barely misses his head. Chuck rolls out of under the desk, as he wraps the mouse cable around Shaw's ankle and pulls. Causing Shaw to fall into the splits. As Shaw falls, Chuck sends a spinning kick towards Shaw's head. Shaw blocks it, but the force causes his head to fall back and hit the desk, slightly dazing him. Chuck follows that with the keyboard, cracking Shaw right at the base of his skull with the edge of the keyboard, and causing Shaw's head to hit the desk again. As he falls backwards, Chuck brings another kick up, and this one connects with Shaw's forehead.

Shaw falls to the floor, knocked out.

Chuck rushes over to the panel and opens the door. Getting a rushed embrace from Sarah, and a pat on the shoulder by Casey. "You did good kid. Now let's get out of here with him before anyone else comes." Casey says, holding up some handcuffs.

The team gets Shaw handed over to Beckman's trusted transfer team, and filing the paperwork to list him under private John Smith for designation to a black site. Not even they would know where he was being sent. They all got together for a family dinner. Justice had been carried out.

Sarah knocked on Chuck's door. They hadn't gotten much of a chance to be able to talk since Shaw had taken her the first time. And most of the time they had spent together hadn't been spent talking. It was communication, just of a different kind. Sarah thought with a slight grin to herself.

Chuck opened the door and let her in. Giving her a kiss, he asked, "Hey Sarah, is everything ok?" He could read a slight pensive look on her beautiful face.

"Chuck. I feel I owe you. I owe you a story. My story. The truth as far as I can remember. You see. None of those files you have will tell you the entire truth. Because from the start, none of them had it. You see, part of why I chose this cover name for my CIA contracts is because, my real name is actually Sarah. Sarah Lisa Kowalski."

Shaw sat in his cell. The trauma to his brain while running the Intersect had done its damage. He struggled to focus on anything. Anything except his hatred. That ran too deep to be subverted to anything else. Hatred for the CIA, hatred for the people who were supposed to be looking after him. And most of all hatred for Chuck and Sarah. He hated them most of all. He knew lunch time was getting close. The only interaction with other people that he ever got now.

A figure made its way to the seemingly abandoned building. Scanning their badge and walking into the door. They walk right past the guards, who look at them and then go back to what they were doing. They walked right to Shaw's cell and open the door.

"About time you got here. I've been wait.." Shaw frozen. He looked into the dead eyes. He looked at their ashen skin. The life seemingly drained from them. The figure raised their arm, and Shaw was left with the sight of a lifeless walking corpse and the flash of a barrel being the last things he saw.

Three shots. One in his head, and two in his chest. They say, "We are done here." And the figure turns and walks out of the black site. Leaving the cell door open.

A/N: So now Shaw is dead. Though it still will be a while before the team knows. Heck of a way to go though. Let me know your thoughts. Who's the shadow?