Why weren't the good guys in the Intersect?

There were a few exceptions. Sarah was in it, Chuck's Stanford file was in it, and Casey was in it as Alex Coburn. Carina and Casey's girlfriend were also in it. I think it would have probably been helpful for Chuck to know who he's dealing with, even if the person is not an enemy, because a lot of times, the people he thought were friends turned out to be enemies. Now, I'm not talking about civilians, but CIA and NSA agents, FBI. Also, judging from the first few episodes of the series, the CIA and NSA don't seem to exactly get along very well, so it might be prudent for Chuck to be able to tell them apart. I guess you can't get too carried away or else he'd be flashing every few minutes or so, which can be both harmful and distracting, but at least have some of your more important people in there.

He thrusts his fists against the posts and still insists he sees the ghosts