A/N: Hello thought I would follow this idea I had for a new one. This is an AU in the time frame of the start of S3, original story. Chuck has intersect 2.0, but doesn't do the whole NEO from the matrix thing. Once again don't own or make any $ from Chuck.

The young woman stood outside the room and waited to be summoned inside for her inquisition. Her gaunt figure and haggard appearance suggested that she was nearing her physical limitations, and in desperate need of rest. She was hoping that the people inside would finally release her from her indentured servitude to them, and accept her work as penance for the sin of ever joining their organization. She had jumped at the chance to join them years earlier, when she still had a naivety about the world and they offered unlimited opportunities and cutting edge research. Now that impression was a distant memory as her body stood as a testament to the harsh reality of the world.

She had foolishly gone back to them for help after her arrest and, after getting her out of prison; they conscripted her to design an instrument of death. The last few months had been exhausting as she spent every day locked inside a secure laboratory working on a project that she hoped would release her from the hell she found herself in.

"They will see you now," a nondescript man said who opened the door.

She walked into the darkened hall alone and jumped slightly when she heard the door close, then waited quietly for them to acknowledge her. The room was completely dark, except for five silhouettes that were waiting behind a table.

"Welcome back Ms. Roberts. We understand that you have made progress on your research. Is the package ready," a voice said.

"Yes," she replied.

"Excellent. Shall we commence with the test?"

Immediately a television screen behind Jill turned on showing her lab assistant Trevor, in a sealed room strapped to a chair. The fear in his eyes was evident as he struggled in vain to free himself.

"I have made the preparations as you stipulated, but I request again that we don't do the test. I know the package works," she pleaded.

"We must be sure that the package is operational. You came to us for assistance, which we provided and now we must be assured that you have completed your assigned task. I'm afraid that the current circumstances warrant a test. While we appreciate the gravity of the situation, a negative test will negate your usefulness."

"But I can show you all of the simulated results," she begged.

"And what good would that be without visual proof? No the test will continue,"

the voice replied.

"But please..."

"Commence the operation," the voice said.

Immediately the screen began to haze as gas was released into the room with Trevor. His body began to convulse against his restraints violently as the poison made its way into his lungs. The poison that she designed was a variant of the neurotoxin tetrodotoxin (TTX), which she extracted from bacteria found inside the blue ringed jellyfish. Using her training as a biochemist she was able to amplify the TTX while Trevor was able to find a way to nebulize it, creating a very deadly gas. Jill stared in horror as their creation began to destroy Trevor. His body appeared to be melting as his violent convulsions, and frothy mouth, coupled with his blistering skin filled the screen. His anguished cries pierced the silence of the observation room, until finally his suffering ended.

Silence gripped the room, as Jill stood shocked at the savage nature of her creation.

"Well done Ms. Roberts! You did it," the voice congratulated her.

Jill was physically ill from witnessing the macabre and grotesque scene. She suddenly wretched as the realization of what she just created took hold. After depositing what had passed for her lunch in the trash can, she turned on unsteady legs to face the panel.

"I have done what you required. Please let me go," Jill begged.

"I'm sorry Ms. Roberts but you are only half way there. You have successfully made the weapon, but now you need to fulfill the promise you made to us."

"Please I have done what you asked, don't make me do this," Jill pleaded.

"I'm sorry Ms. Roberts, but a promise is a promise. You need to keep your word. You need to kill Sarah Walker."

"Yes sir," Jill replied.

"That is all Ms. Roberts," the voice said as a man appeared and led Jill out of the room.

"Our fortunes seem to be turning, now we begin or operation," the voice said.

Sarah awoke from the most satisfying sleep she had in years. She heard Chuck still snoring away and just silently looked at him. He looked very peaceful as if he hadn't a care in the world. It was a little unnerving for her how strongly she felt for him, she could not imagine what she would have done if those ring agents had shot him. She was only certain of one thing, that if he was dead then she was dead as well because that's the only way they would get to him, they would have to kill her.

When did this happen? When did she become so possessive and protective? What has this guy done to me?

She thought back to those fateful moments over the past year, which spurred her to action. After seeing him dropped off of one too many buildings and blown up in one too many cars, she had finally had enough and decided to confront her feelings for him. She knew that she was in love with him, but after seeing how close he came to dying so many times, she was determined to keep him safe; and in her skewed view of reality, that meant to end any romantic feeling they had for each other. She rationalized that the feelings she had for him clouded her judgment and made it almost impossible to stop thinking about him, which when on a mission would ultimately lead to failure. Her failure. She couldn't live with that, she could never live if because of her failure he died. She needed to keep him safe above all else, and if that meant that she would have to sacrifice her happiness then that was what she would do.

A week after he downloaded the intersect 2.0, and after finally laying the ghost of Bryce Larkin to bed, she came to his apartment to confront him. Her plan was very simple, just state her position clearly that she didn't love him and they would never be together. Twelve hours later however, her plan had clearly changed as her position was now underneath him as they passionately made love for the 5th time that day. After that there had been no going back for both of them, they were in love and there was no point in denying it anymore. They told Casey about it, and Sarah found him surprisingly human about it, he was only concerned with not having to play wet nurse to a broken hearted Bartowski; a scenario that Sarah assured him was an impossibility.

They tried to hide their relationship from Beckman, but eventually Beckman would find out and Sarah would have to deal with the fallout. She would have to be ready to get him at a moment's notice, which is why she had been preparing for such a situation. She had enough money stashed away to last a year, maybe 16 months if they stretched it. She had bags with new clothes and identities for her and Chuck as well as 4 safe houses established in Europe.

She was just about to creatively wake up Chuck, when an alert from her phone went off.

Report to castle immediately. Do not inform Chuck or Major Casey…Beckman out

The feeling of dread that descended on her was crushing, and her first inclination was that Beckman had found out and she would be reassigned. She debated taking Chuck off the grid right now, but she realized that there were too many variables with that scenario. She didn't know what she was up against, nor how much Beckman knew. A million thoughts were going through her mind as she slipped silently out of bed, and into the night to get to castle.

Does she know? Had she been reassigned? She thought.

They had just finally started a relationship after all they had been through and even though she was unsure of what Beckman wanted, she knew one thing for certain, she wasn't going to give him up and she wouldn't allow the general to reassign her

.

"Thank you for coming agent Walker. I am sorry about the secrecy but I needed to talk with you privately in regards to an urgent matter," Beckman said.

"Yes Ma'am," Sarah said.

"It is in regards to Mr. Bartowski," Beckman began.

Immediately Sarah feared the worst and tried to control he emotions as Beckman continued.

"Sarah we have learned of an assassination plot against Chuck," Beckman began.

Sarah shuddered involuntary.

"General I should be with Chuck, do we know the identity of the assassin," Sarah rambled.

"Sarah Casey has secured Chuck back at his apartment. I needed to talk to you because the contract was placed by a former girlfriend of Chuck."

"General do you mean…,"

"Yes Agent Walker, the contract was placed by Jill Roberts. We believe that she did it after her escape from prison. At this point we don't know exactly who has the contract but we are working to find out."

Jill ..that bitch I'm going to fucking kill her!…..Sarah fumed

"General I assume I will be assigned for protection, and why was I ordered not to tell Chuck or Casey," Sarah said.

"Agent Walker given the nature of your relationship with Chuck, I wanted to ask your opinion of Bartowski's mental state," Beckman said.

"I'm sorry ma'am I don't understand the question," Sarah replied.

"What I want to know is if Jill Roberts is still a blind spot for him?"

"Chuck is a very loyal and forgiving guy, he tries to see the good in everyone. That quality can get him into trouble sometimes, as it did before with Jill. However even though he is too naive for his own good sometimes, I can assure you Jill is no longer a blind spot for him."

"Is that your assessment or is it a fact?"

"I can assure you it is a fact ma'am," Sarah replied.

"You seem very confident Agent Walker," Beckman said.

"I am ma'am," Sarah replied.

Sarah was confused as Beckman had a slight smile on he face.

"I'm sorry ma'am I don't understand your reaction. Am I not understanding the situation correctly," Sarah said.

"No you are, I just hope your boyfriend does," She chuckled.

"My boy friend ma'am? I'm sorry…,"

"Save it Walker. You may be a good actress, but you two trying to hide this relationship is like seeing Casey at the DNC convention," Beckman scoffed.

"Why haven't you said anything? Why haven't you split us up?"

"Because this team works well together. I see no reason to break it up, provided that everyone can play nice with each other," Beckman said.

"Yes I can assure ma'am it will not be a problem," Sarah said as she felt the relief wash over her and the weight of the world lifted off her shoulders.

"Good. Now we will threat assess the situation and determine the appropriate level of security for Chuck. In the meantime you are assigned to round the clock protection of Chuck."

"Understood ma'am. What are your orders for Jill Roberts" Sarah asked.

"If she should surface and she can't be brought in, then terminate immediately. "

"Understood ma'am," Sarah answered quickly

"Agent Walker I said IF she can't be brought in. Do you understand?"

"Yes ma'am," Sarah said with a hint of frustration.