AN: same old disclaimer own nothing not gonna make a cent. Thanks for those that reviewed. Please see AN2 at the bottom. More big reveals and more of Chuck's past. I always felt Ellie needed to be more involved so….Now please start reading!

Chapter 7

The rest of the month passed without much fanfare. Mission wise it was flat out boring for all the remaining agents within the ISA headquarters. A good majority of the agents that worked for Chuck at the ISA were out on missions. Most of them conclude within the next couple of weeks, if not sooner. The ones that had completed their missions were assigned to desk duty. Chuck was a firm believer that after a mission, no matter how long, his people needed time off to relax and decompress. He even arranged counseling for those agents that felt they needed it. This again surprised Sarah. While she was actively working for the CIA she was often sent back in the field without a decent break. The more she witnessed Chuck's operation, the more she understood why his group of agents had such a high success rate. She also found out that the agents that worked for Chuck were still with their respective agencies. They may get their Intel from Chuck's group, but the missions they went on were given to them by their agencies. In essence Chuck was their handler.

The relationship between Chuck and Sarah was going well. With both of them pretty new to the relationship business they were taking it slow. They got together a few times each week for dates but gave each other time off the majority of nights. Neither of them really minded, after all they did see each other at work. Another thing that was bringing them closer together was the training they did together. They would go on morning runs with each other for their cardio. To make it more fun they would often change the venues for the run. Being in California did have its perks, one of them being the number of public parks that featured running trails. They would spend time in the gym lifting weights and every few days they would go to the dojo and practice their hand to hand skills on each other. During their sparing sessions no quarter was given or received, but Sarah knew that Chuck was holding back. Despite her desire to win, she looked at for what it was, a chance to improve her skills. Every couple weeks they would head down to twenty nine palms to work on their sniper skills.

One big development that happened was Morgan called Chuck to play Call of Duty. Both of the men had fun and some of the tension from before was eased. Chuck knew their friendship would never be the same, he was just glad to have his friend back in some form. The holiday went well for all parties. Ellie invited Morgan and he accepted.

December 2006

With the holiday over and after a few long talks with Ellie Chuck made a very hard decision. It came about during one of his longer chats with Ellie. She let Chuck know, in no uncertain terms, that he needed to tell his girlfriend the last big piece of the Chuck Bartowski puzzle. The information he planned to reveal was so secret, there were only four people in the world that had access to this information and none worked for a three letter agency. Sarah would make the fifth person. Chuck and Ellie escorted Sarah into his personal office. It was the largest of all the offices and was complete with a gaming consol. Once they got comfortable Chuck, with Ellie's help began filling her in.

"I'm sure you're wondering why the ISA has such a big server room."

"It does seem quite massive for the number of computers we have in the building," replied Sarah. "We have at most one hundred agents here at one time. A regular server could handle that many."

"In a normal office that would be true." Ellie added in. "Have you ever heard of the intersect project?"

"Just some rumors about a top secret project but nothing concrete. Why, what is it?"

"After nine eleven the intelligence communities tried to come up with a way for all the agencies to share any information they had." Chuck piped in. "On paper it looked good. There was a problem with the idea however. They failed to take into account the human factor. The Directors of each agency are basically greedy bastards, needing to be on top so they began to withhold information hoping to remain on top. They each wanted their ace in the hole so to speak."

While Chuck was speaking he called up a diagram on his computer and put it on the monitor on the wall. It was shaped like a spoke wheel. In the center there was a picture of a computer. Around the computer were other computers. Each of the outer computers was connected to the one in the middle.

"This is how the Intersect was supposed to work with each agency having access to all the data. Each agency would input their data into the mainframe or Intersect. That would allow the other agencies access to that data. When that didn't happen the Sentinels got involved for our own sake. We created a pipeline to the data each agency had. Every time data is inputted to any of the main frames we get it as well. We have a program that filters out overlapping information. It saves room on our servers. We have all the Intel this country has at our finger tips. This," he said point to the server room, "is the only true intersect." Chuck reached for the drink on his desk and took a long pull from the glass. This gave Sarah a chance to ask some questions.

"That's why we have so many analysts up stairs. They sift through all the new data and put the information into a workable form. If I may say, that is amazing."

"It is. There is more," said Ellie. "Right now the NSA and CIA are trying to build their own version of the Intersect. The CIA has other plans for the intersect however. Have you heard of project Omaha?"

"I was on the project. When the project got mothballed I got partnered with Bryce. I'm still not sure what the end result was supposed to be," stated Sarah.

"While the NSA the uses the computer to find clues in the data and extrapolate the data and pass on that information to the agents," Ellie continued on with her explanation. "The CIA is taking a different approach. They want to put the intersect into a field agent. That way the agent would have all the information with them. That's what project Omaha was about. The CIA planted an agent in several collages around the country. One was at Stanford, Professor Fleming. They gave all the students in Professor Flemings' class a test. It was designed to test a persons' ability for subliminal image retention."

"Chuck is that even possible? And if it is why did they mothball the project?" questioned Sarah as she looked over at Chuck.

"It is. It was mothballed because they couldn't find a suitable candidate. When I was at Sanford I graduated a year early. My "senior year"" Chuck used air quotes as he said it, "was my cover for an operation I was working on. Smith got word of project Omaha during my actual senior year and kept me there to monitor the progress. I was roommates and friends with Bryce."

"Bryce Larkin, my old partner was your roommate?"

"Yeah he was. He found out what my test score was and thought he could protect me from being recruited by the CIA. He didn't think I was agent material. He didn't know I was already in the Sentinels by then. He planted evidence in my room that proved I cheated on the test and got my score thrown out. He then proceeded to break me and my girlfriend Jill up by sleeping with her. That gave me the perfect excuse to leave town with my head hung in shame, in that way it worked out."

"So Bryce screwed you over to protect you? I can understand his motivation, even if I don't agree with it. I know when I first met you I didn't think you were an agent, let alone an elite one," Sarah explained.

"If that was the only reason it would be," this time Ellie jumped in "Bryce had other motivations for doing it. His test scores were borderline acceptable. He figured by getting rid of Chuck, he would take Chuck's place. You were going to be his partner. Egotistical prick that he is was looking for fame and glory like when he suckered you into the ill-fated mission. He needs accolades and will step on anyone in his way."

The more she heard about Bryce the madder she got. She couldn't help but blurt out, "That self-centered son of a bitch. He got me benched because he wanted to make a name for himself. Next time I see him I'm gonna kick his ass."

"You get to him first. I plan on killing him," Chuck interjected. "To get back on subject they had a candidate, me. My scores were above what were needed to host the program. I would have been your partner if they got it working. Without me they scrubbed the project. Now comes a bit of history. I'll make a long story short. Before I was born my dad was part of the original project. It was designed to input a personality into an agent for missions. The CIA believed it would make the agents cover better. The plan went pear shaped when a colleague of my father's tested it on himself before it was fully checked out. He became Alexi Volkoff. It took my dad years to figure out who Volkoff really was." Chuck again paused to take a drink and stretch his legs.

"Wait," exclaimed Sarah. "The most powerful arms dealer in the world was created by the CIA?"

"That's correct." This time it was Ellie. "When Chuck was about eight, he snuck into our dad's office and downloaded an early version of the Intersect by accident. It was around this time the CIA figured out that they had created one of the most vicious criminals in the world. They went after our father thinking it was his fault. My dad left to protect Chuck and me. He keeps in touch even though the CIA is looking for him. He kept working on the project, refining and improving it as technology got better. That's where I came in. I knew Chuck was part of Mossad and had downloaded the program. My dad made a huge mistake in his programing. He's a computer geek just like Chuck so he made the program to work in the brain like in a computer."

"I prefer nerd El."

"Hush Chuck I'm speaking. Now where was I before the geek interrupted me? Oh right, the programing. The problem is the brain doesn't work or store information like a computer. After I looked over his programs I point out where he should make the changes, and he did."

"After I became a Mossad agent he began sending me updates to his program," Chuck added. "Thanks to Ellie's help he got the bugs out of the program. That's another reason we weed out the duplicate files. Uploading the Intersect into agents works, Sarah, I have all the governments intelligence data in my head, I'm the human intersect."

This was just a bit much for Sarah to handle. Hers eyes rolled back in her head and it took everything she had to keep from passing out. "You're the Human intersect? How is that even possible?"

"Yes I am. I just used the thing; I don't worry about the details. That is for Ellie and Orion, my dad to work out. That is how I knew you were CIA when you busted up my card game. Certain things will access the data. It could be a name, face, scar, voice or a tattoo. We call it a flash when I see the data. It distracts me for about a second. That's why Larkin could get the shot off."

"OK Chuck, prove it."

"What do mean prove it?"

"You have to understand that was a lot to take in. I trust you and Ellie but I need to see how it works."

"That's a tough thing to do." Chuck mulled some ideas around before he spoke again. "Your last mission with Bryce, the one you dropped to shoot me, what was the name of the guy you were after?"

"Pierre Marquis." Chuck's eyelid's twitched and one eyebrow rose slightly and he began to speak.

"Born in France. Graduated from UCLA, has connections to a terror cell in France. Claimed responsibility for the bombings of the French rail system in 2004. Wanted by Interpol on murder charges. There is more but that should do."

"Damn." Sarah was stunned. The implications of what the human intersect could do was staggering.

"Chuck, just how much do you know about me?" she was getting nervous. After a second she relaxed. Even if he did know all her sordid details, he still asked to go out with her. She already knew Chuck was special, now she knew exactly how special he is.

"Pretty much everything that's in the CIA data base. Don't worry I can stop a flash when I have the information I need. I have been using the Intersect for a long time. I learned to control it a year or so ago. Ellie and Orion have advanced the intersect so much I can access the data base by just thinking about something. I stopped when I saw you are with the CIA. So don't worry about that. I figure when you're ready you'll tell me."

"Thank you for that. In time I'll tell you, I'm just not ready for you to hear it from me."

"No problem. One last thing, the CIA is looking for my dad. Our cover is we don't know where he is."

"That works for me. Why don't we take a break and go to lunch. I really am hungry."

"I could go for some food," added Ellie. "Besides you have the basics of what we do here. The rest he can fill you in on later or when it comes up. Let's go eat." This was said as she was heading for the door.

"You two continue to surprise me every day," Sarah said to Ellie as she caught up to her in the hall.

"Why is that?"

"When we first met I was shocked you knew about Chuck being a spy. Now I find out that you and your dad worked on the intersect together. Is there anything else you wish to share?"

"Not at this time except that I'm not as innocent as I look, and Chuck is far more dangerous than he looks."

That final remark made Sarah wonder what kind of situation she had the luck to fall into. From what she could tell it was a family of spies, one she was glad to be a part of.

They grabbed a couple of sandwiches at a local deli and went to a local park to eat. It was nice to get out of the office and hospital for a change. The time away from the office gave Sarah a much needed break. She was still trying to wrap her head around everything Chuck and Ellie had told her. She was pretty much in awe with Chuck and how he handled the fact he was the human intersect. He was so nonchalant about it. She wasn't sure how she would act if she had the same responsibility he did. She was even more in awe of Ellie. Sure she was a neurologist, and that was way above what she expected when Chuck told her Ellie was a doctor. Now she had to factor in that Ellie was a computer nerd as well. It simply amazed her that both the people she had come to love had such a secret life and nobody else knew. That was simply astounding. They cruised around the park for a few minutes before heading back to work.

Ellie headed home to tidy up the house while they returned to the war room. After they entered the headquarters they headed in the direction of Chuck's office when a light mounted on one of the monitors began to blink. Sarah didn't know it yet but she was going to witness her first mission request call. Several things began to happen at once. Agents that been sitting at their usual desks got up and moved around switching seats. The ones that didn't sit back down left the room. While this was happening Chuck turned to Sarah and said, "Beckman's calling in."

"Physic now as well," as she raised an eyebrow.

"I'll explain after the call." He nodded to an agent who accepted the call. The General appeared on the monitor, "Good afternoon Ma'am."

"Afternoon Chuck, I have an urgent mission that requires special handling. One of my best agents has gone missing. Major Casey was getting ready to move in on an Al-Qaida cell in Pakistan when the mission suddenly went south. We lost his team's signal half an hour ago. I don't have to tell you those Bastards don't play games. I need you to pick out my agents and put together a team to get his ass out of there."

"Roger that Ma'am. You need to have transportation waiting for them at LAX. Send me all the information you have, last know grid co-ordinates and the locator beacon's frequency. The team will be there within 2 hours. The plane must be able to be refueled in flight and have two flight crews on board. I don't want them wasting time getting them out of there."

"Thank you Chuck, tell my team happy hunting. Beckman out." The screen went black the moment she ended the call.

"Chuck would you please explain what just happened. Quite frankly I'm a bit confused," said Sarah. Chuck led her into his office before explaining.

"Sure. I told you I would explain as we went along. The three large monitors are for the CIA, NSA and FBI. The two smaller ones on the side are for Home Land Security and the DEA. For some reason none of the agencies trust the other agencies agents to do their job. Depending on whom calls in the agents in view are from that agency. The NSA agents filled in those seats because it was Beckman. The agency heads think I'm their agents' handlers. We know different."

"Seems weird to me but if that's how they play I'll understand."

"If Graham calls in you will need to sit at one of the desks as well. Normally the Directors will ask for the agent they want to handle the mission and I make it happen. If they tell me to put a team together, they want Ghost. None of Directors know his name or who his boss is. They think I'm his handler. They call me to get in contact with him. One of the reasons I work from home a lot is to avoid suspicion. Before you became my partner I was never here. Granted I only spend a couple of hours a day here so they don't miss me when I'm gone."

"So I'm your partner now?" Sarah was positively giddy with excitement. She was going to be working on a mission with the Ghost. What a huge step up from the rat bastard Larkin.

"On most missions yes. There will still be some I need to do alone. Not that I don't think you can do the job, sometimes it's better if I go alone."

"Fair is fair I suppose. So when do we leave?"

"As soon as I get all the information and let Ellie know. I'd say about half an hour."

True to his word they left in half an hour and headed to the airport. All they had to do was wait until they were ready to jump. They both knew it was gonna be a long flight.

AN2: this is to clear up any confusion that my use of handlers may have caused. There are two types of handlers. One is like Sarah and Casey. They work with someone not in an agency, like Chuck. The other is one that works with an agent. Agents need to report in and get assignments. They get this information back and forth through a handler. Handlers will set up meet locations, safe houses plus other things. I hope this cleared up any confusion I might have caused.