Sarah was confused. It seemed to be happening a lot lately, what with the Chuck/staying professional argument that was constantly raging in her mind. It said a lot that she was counting the unprofessional side of the coin as "Chuck", when in reality he was essentially her job, at least for the time being. More than once she had caught herself thinking about her asset in very un-asset-like terms, and yet it didn't bother her so long as those thoughts remained in her head and weren't expressed. It was too early for her to be compromised. She couldn't be, surely?
And then there was the disk that Team Bartowski had recovered from Stanford. Sarah had to admit that she was intrigued by what had caused Chuck to come onto the CIA's radar while he was at college, and now it had come to light, she understood more fully what Bryce had meant by being "forced" to destroy his best friend. What had thrown her was that if he had a reason for getting Chuck expelled from Stanford, maybe he had a reason to go after the Intersect? Maybe he wasn't a traitor after all?
That was where Sarah stopped her line of thinking. She trusted her agency; if Bryce was a traitor according to them then he was probably a traitor. Unless there's a rogue group within the CIA, but that's impossible, thought Sarah. She had heard stories from her instructors that there had been a rogue group within the CIA, but in this day and age? The vetting process alone should have taken care of that. But if Bryce wasn't a traitor, then why didn't he trust her? She could have helped him.
The hammer blow was the name of the project Chuck was being recruited for. Omaha. Where she and Bryce had first met. He was the best prospect from that project; to upload selected data in the form of subliminal images into an agent to provide intelligence for a specific mission. The project had been scrapped once the casualty rate got too high, but Bryce's subliminal image retention was supposedly high enough to survive a partial download of the Intersect, which was why he had been partnered with the rising star of the CIA: Sarah Walker. They were going to be the prototype Intersect team, before the scrapping of the project and the turn to a computer based Intersect.
Now she found out that Chuck would have been on the project. He would undoubtedly have been the prototype Intersect, going on his retention scores for subliminal images, which meant that she would have been partnered with him instead of Bryce. And there wouldn't be any need for this damn cover maintenance. We could have been real.
With the thought of how she was only a single badly timed meeting at Stanford away from a real relationship with Chuck, yet she was now stuck with playing a cover girlfriend/bodyguard to a man she had, against all odds, developed feelings for, Sarah looked down at the disk in her hands and tried to stop the tears of loss.
CIA rule #2: Don't let your asset see a moment of weakness.