An episode like "Chuck Versus Agent X" makes you think what would have happened if NBC had just given Chuck a full season order instead of a 13 episode season and adding episodes after all the new shows tanked. And, given Chuck's current low ratings, we may never know how the writers would deal with a full season beyond the second.
"Agent X" is one of those episode which makes you think several times, "Hey, couldn't this be an episode by itself?" First, there is the bachelor and bachelorette party which certainly could have been extended to a full episode, but it's forgotten by the second half of episode. Second, Ellie finally learns of Chuck being the Intersect and they have a heartfelt scene together, which could have ended an episode. Third, Sarah, Chuck, and Casey go to England to find out who Agent X is, and after recovering his box, learn that he is Alexei Volkoff.
This makes for an interesting, if not unexpected, twist. There is the obvious problem of Vivian actively hunting for her father (though I still don't understand why she thinks Agent X is her only obstacle to world domination), but there are plenty more issues this bring up. Casey, Sarah, and Chuck have been intimately shaped by the CIA (and the NSA in Casey's case) and have become different people than when they first entered the organization. But none of them entered in a truly voluntary manner. Casey joined the NSA because it was the next best option, Sarah joined because she wasn't in the best situation either, and Chuck was pretty much forced to go along with the CIA. In a way, they represent a less stringent form of what happened to Volkoff, who changed because his brain was actually altered.
Score: 8.9/10