A/N: The show alluded to a Project Omaha but never revealed any real details. Perhaps that is why so many of us who write gravitate to the idea of the project as a playground. Well add me to that list. It gave me the ability to play with some ideas, set the stage for future stories, and to explain away a portion of the show's story line I disliked: Bryce always returning. Don't get me wrong, I understand why that element was there, to keep the will they, won't they tension everyone enjoys so much, as long as it does not drag on season after season.

Chapter 12 - Omaha

"Mom, what are you saying?"

"Everyone sit down. It is time you know the whole story. I don't think it will change your relationship with one another, but it may change any plans you have to use the Intersect on Sarah."

As everyone starts to sit down, Mary grabs John by the arm, "Agent Casey, I need to know where your loyalties lie? Are they with my son and his wife, or are they with the NSA?"

John looks at Mary and grunts. He doesn't like when people challenge his loyalty to America.

Almost as if she speaks Casey, Mary responds, "John, I'm not asking about your loyalty to this nation. No one questions that, but what I need to know is, can I tell you guys the type of secrets that get people killed, and trust that should an order come down, you would choose all of us over that order."

"I'm loyal to the nation."

"What if loyalty to that nation went against orders?"

"I will protect my team and their families."

Casey had already proven this by letting Chuck and Sarah both go on numerous occasions. However, on each occasion the outcome hid the fact. Yet, Mary should've recognized this since she was with him when they stood against Decker to save Sarah from the Norseman Device.

"Ok. Please turn off all recordings of this area."

Mary watches John disable the cameras and audio feeds.

"Good. Now where to begin? I guess we should start at the beginning. Chuck before Ellie or you were born, I was assigned to a top-secret project called Operation Pedagogue. Remember I told you the original intent for the Intersect was to teach people."

Mary takes a seat and stares out for a moment.

"I was a young CIA agent being assigned to one of the top teams in the agency. We were being tasked to provide security for two scientist, an American and a Brit."

Mary smiles a small smile.

"I remember the first time I saw your father. He was so handsome. He looked like that actor on that show you used to watch. You know the show about the doctor who time traveled into other people's lives and looked like them?"

"Quantum Leap." Chuck smiles.

"Yeah, that was it, how unbelievable was that?" Sarah shakes her head.

"Yeah, kind of like a computer downloaded into someone's brain? The story, mom?"

"Oh, yes. Well we soon discovered we could plant an identity into someone. Anyways, we all know how that turned out. So from this point forward, everything I tell you comes from your father's covert Orion work and data collection."

She takes a deep breath. This is not going to be easy.

"After Hartley and I went off grid into our covert roles, your dad lingered on the project for a while, until he learned what the ultimate goal of the project was at the time: a full team of human Intersects. They were experimenting on what the retention threshold would need to be to safely host the Intersect in each of it's forms."

"Forms?" Casey asked with furrowed brows.

Mary gave a very tight-lipped smile. "Your dad and a few others wanted to divide the Intersect into three models: a data only model, a skills only model, and the complete package."

"What kind of experiments?" Carina asked while narrowing her eyes.

Sarah did not like the word experiment tied to Chuck's knowledge that she had worked on the project. She had to know.

"Chuck, are you sure I was on the project? If so, why don't I remember that? It would have been years before being assigned to you. Quinn didn't erase my memories that far back."

"Chuck, let me answer that." Mary looked at Sarah. "Sarah dear, you did work on the project. Stephen had entire files dedicated to you and some of your peers. It is one of the reasons he asked Chuck if you could be trusted."

"Mom, I never doubted Sarah and I told Dad I trusted her with my life, and when I said that I meant more. I trust her with my heart."

"I know dear, but let me move on and both of you'll understand his concern, and why some of the things have happened to you."

Carina stood up. "Anyone want some popcorn, this is getting entertaining?" No one smiled. "OK, bad joke, but still I want something to eat. Does anyone else want some?"

"Sure, I'll help." Casey stands to join her.

Mary watches them for a few moments like she is waiting on their return.

"Mary, please continue." Sarah is anxious.

"Fine. Sarah, before you were targeted for recruitment, the project began to use chemical enhancers to force physical and mental thresholds higher and to increase the likelihood of success."

Casey and Carina rejoined them. "You mean they were really trying to make the six million dollar man and woman? Minus the bionic body parts." Casey asks.

"You could say that. They discovered that if a person had a certain level of physical and intellectual capability they could push them further by injecting them with a chemical agent. They also discovered a side effect. It made the agents susceptible to memory suggestion and with the right triggers they could erase a person's memory of an event, or even whole time periods. This chemical compound was eventually diluted into what we call X-13."

"Casey, I told you that stuff was dangerous." Chuck looked at him with raised eyebrows.

"Chuck, didn't you just tell us to use it on Kayla Hart?" Carina defends Casey. Casey smirks, and Sarah looks at Carina with surprise in her eyes.

Carina smiles at Sarah, and raises an eyebrow.

"Children! That is beside the point. They discovered that an incomplete Intersect would have the same effect. As well as the Intersect in the wrong person, or an over active Intersect in a person with proper thresholds."

"So how'd they overcome the problems?" Chuck asked.

"They never did. A person with a proper capability level could handle either the data package or the skills package. To date no one has been able to handle both."

Sarah speaks up, "Chuck is capable of handling both." She then looks at Chuck with loving smile.

"Really? Chuck, please take off the governor your father built." Mary gives an implied command.

"No, he can't!" Sarah reaches over and stops him by placing her hand on the watch.

Mary was watching her closely. She noticed the moment Sarah touched the watch her body relaxed a little.

"Sarah, you can feel the calming effect of the governor, right?"

"Yes, I noticed when I first gave Chuck the watch." She started to turn her head toward Chuck but couldn't look him in the eye.

Chuck looks at her and holds her hand. "Why didn't you say something?"

"Because I didn't want to hope that it might help me, when I could've been feeling relief because I found it, and you'd soon be out of pain."

"I love you!"

"And I you!"

"Alright, enough! Mary, please continue before we all have to leave the room and you become a grandmother." Casey sounds a little annoyed and uncomfortable.

"Nice John!" Sarah is annoyed.

"Casey's right, I need to continue before someone tries to relay into Castle. By the time you kids reached college, they had the threshold determined. They sent recruiters to college campuses and certain high schools were the student's scored high enough on standardized tests."

"I always knew those tests were for more than measuring educational progress." The conspiracy theorist in Chuck just raised his head.

Casey grunts and Mary shakes her head.

"Students who exhibited certain capabilities were targeted. If they could not afford college, scholarships appeared. Chuck, that is why you and Bryce both ended up at Stanford on scholarships. Sarah, we know how you got selected. Your dad's dealings almost interfered with them recruiting you, so Graham compromised your father and him arrested."

Everyone is looking at Mary and not talking. Suddenly everyone realizes how seriously commitment the clandestine heads of government were to seeing the Intersect deployed in the field.

"Like Sarah, Bryce was recruited out of high school. He was considered a pre-candidate, much as you were Sarah, through his sophomore year. However, that didn't mean he was not tasked with certain jobs, like getting close to Jill Roberts and Chuck."

You could feel the room temperature rise around Sarah.

"That is where things began to go sideways. Sarah, you were confirmed for the project during your junior year."

Mary took a deep breath.

"Here is the tough part. The CIA wanted to put together two sets of young couples under a paternal type of handler. Agent Quinn was selected to be the Intersect handler leading the two sets of couples. Quinn began the enhancement treatments, but was captured before an upload could be conducted. He felt cheated, and we all know how his part in this story ends."

"Why would they want couples with a 'paternal handler'?" Chuck extended his arms with his palms forward like he was ready to receive the answer like a package.

Mary bows her head and doesn't look up. "There was a married couple before you guys. Even with the drugs she suffered catastrophic results during the upload, and he sought revenge against the agency."

"By catastrophic results you mean she died?" Sarah asked with a sad countenance.

The silence was her answer.

"What happened to the husband?" Chuck looked like he might've been thinking about Sarah and him.

This time Mary looked up and spoke. "He was arrested and dropped in a dark hole. He was probably remanded to a super max somewhere. This was only about four of five years before you guys."

"Ok, what about Sarah and Bryce?" Carina is really curious. She never understood the draw Sarah and Bryce had toward one another. If it were just sex they both would've moved on easier than each did.

"Yes, well. They were slotted to be an Intersect couple. Chuck and Jill were slated to be the other couple. Bryce helped identify Jill as a potential, but she was recruited by Fulcrum who concealed her capabilities. The good professor identified Chuck, but Stephen and Bryce devised a plan to keep Chuck out of the program. Given the drugs, Chuck might have been the first person to handle both packages."

"Wait, does the governor emulate the drug?" The idea just occurred to Chuck.

"Yes, but without the memory loss side effect. Anyways, the government pushed on anyways. Sarah and Bryce both reported to Quinn's team and began the treatments. They were planted with romantic feelings for each other."

"What? The government tried to make me fall in love with Bryce?" Sarah couldn't believe what she was hearing.

"Unfortunately, yes. Bryce was targeted for the performance model, and Quinn for the intellectual, but most people thought Sarah might be able to handle both. In fact, it was believed that both of you were capable of handling the complete package. That is why they wanted you with another person and not each other."

"Wow talk about you mind bender." Carina was completely floored. Casey was steaming.

"While we've got the camera's off. I'm going to give into my lady feelings for a moment. Chuck, Sarah, you keep fighting for each other. Our leaders may very well be making the most of your situation, but you hold to one another. You've got what it takes to beat the odds."

"Thank you, Casey." They both respond. Chuck with a bit of wavering in his voice, and Sarah with tears in her eyes. Even Carina looked a bit emotional.

"Anyways, when Quinn was captured, they decided to give up on the Intersect couple idea. They used a set of hypnotic cards to trigger the drug's side effects and to remove your memories concerning the project. They separated you for a time period. Sarah went to work with the C.A.T. squad, and Bryce went to deep cover school. They used that training to continue giving him performance enhancers."

"You mean all of Bryce's super stunts were a by product of the drugs? How can that be, he eventually stopped taking them, right?" Sarah always felt a step behind Bryce in combat.

"Sarah, they only reason he could keep up with you was because of those drugs."

"Mom, you know dad once asked me if Sarah had the Intersect. She threw a knife that knocked a hatchet out of mid-air."

"Chuck, Sarah is a remarkable lady, and I'm proud she is my daughter-in-law." Mary smiles at Sarah.

"Now back to the story. We're almost done. Eventually, Graham decided to put Bryce and you back together. The memory erasure always leaves a bit of memory behind, and in this case it was your feelings for each other. That is when Stephen caught up with Bryce."

Chuck eyes narrow as he is deep in thought. Mary notices but continues.

"He convinced Bryce of the truth. That is when they decided to steal the Intersect to keep it out of Fulcrum's hands, but also to stop the experimentation on people. Now you really know why Bryce did all that he did. Casey, it's the question I asked you earlier. Where are your loyalties, to the nation or to the agency?"

"I understand."

"Me too! I mean I finally understand why Bryce told Sarah they always had Omaha. He was looking for a sign of her remembering the project. Especially since she was working on an Intersect team."

Everyone looked at Chuck, and he simply shrugged like his theory was elementary.

"Sarah, when you were sent to the C.A.T. squad they discontinued your treatments. Your feelings were not enhanced, that is why you transitioned so quickly to Chuck, and Bryce seemed to hold on for so long."

Now for the hardest part of all, time to talk about the last few weeks.

"Sarah, Quinn used all this knowledge to turn you."

Mary waited for everyone to compose their reactions.

"He was taking Chuck to his base in Japan to turn him by using the Intersect cards, but when he discovered you had the Intersect, he captured you. He used the cards to make the Intersect flash over and over."

Chuck reached over to hold Sarah's hand.

"He also knew your life and missions, so he targeted specific people and places. When he did this, he stopped the random damage the faulty Intersect was doing to you. However, he could not remove the Intersect, so he suppressed it. He knew if you flashed, it would send your brain the same message that the drugs sent, and you would remember some of what he tried to erase. Remember, it is never completely gone."

"That is why I'm remembering on my own."

"Yes, dear. Your memories are not completely gone, but they will have gaps and at times seem more like a vague feeling or dream than an actual memory."

"Mom where does that leave us?" Chuck is holding Sarah's hand.

Carina has one hand on Sarah's back, and ever since he unleashed his feelings, Casey has had one on Chuck's. The more Mary speaks the more the team feels like a family.

"Chuck, there is a few more things you two must know. Your love is real and it overrode the every attempt to reprogram Sarah's feelings. Next, Quinn never gave up on the Intersect couple idea, and he tried to program Sarah as his lover while he held her captive. I don't think it took, after all he tried to kill her, and she has given zero indication of any emotional attachment. My theory is your love for each other is too strong."

Sarah has a look of terror. I woke up in a nightgown. Why did I never wonder how I ended up dressed like that with Quinn in the room? Oh, please let nothing have happened and please let me being sick early this morning be from sleep deprivation and stress.

Carina is holding Sarah in an embrace.

Chuck places an arm around Sarah and she leans into him and begins to cry out of fear. Her own thoughts were now her tormentor.

Casey gets up mumbling something about allergies making his eyes water.

Mary gives the team time to recover from all the information.

"Mom, let me ask my earlier question again. Where do we go from here?"

"Son, you can let the memories surface when they will. You can remove the Intersect and risk the lingering effects of flashing, basically accepting what she knows now as enough. You can unblock the Intersect, but I would not recommend that course of action."

"Mary, why not?" Sarah is still sniffing a little, but wants to know more.

"Dear, the Intersect could flash, and all your memories would come back, but so would the memories of being tortured by Quinn. It could also trigger more flashes and those would begin to rip apart the memories you've gained in a random manner, or you might lose earlier memories, like your childhood."

"What if we had a clean Intersect that could over write the faulty one?" Chuck hopes Ellie found something.

"Chuck, if what I've read in your father's files is correct, you should be able to unblock the faulty version, and simultaneously over write it with a clean version. However, Sarah will still remember her torture at the hands of Quinn?"

"And the unknown will become the known" Chuck states what none of them wants to contemplate.

"Chuck, do you love me?" Sarah is looking into Chuck's eyes.

"With all my heart, no matter what happened."

"No matter what?"

"No matter."

"Then call Morgan and let's see if any of those glasses had a clean version."

"OK"