We can safely say that in its three and a half seasons, Chuck has had its share of plot holes, but those problems were usually contained to individual episodes or minor details in a longer arc. With this current Sarah undercover arc, however, every step appears to be one plot hole after another, contrived to generate angst between Chuck and Sarah.
Normally, I can write off a plot hole because it won't matter the next week. But the entire plot of "Chuck vs. the Gobbler," minus the Ellie stuff, makes little sense logically, and the characters are acting as irrationally as ever. Most importantly, the episode is crucial to the overall plot.
I'm not going to cover everything, but this is what bothered me the most: If the ultimate goal is to bring down Volkoff Industries, why didn't Sarah shoot Volkoff when she had the chance, and why didn't Sarah and Mary do something when Volkoff downloaded Hydra onto another machine? Even if Hydra is the heart of Volkoff industries, isn't Volkoff himself the brain of the corporation? What was the point of orchestrating the prison break actively using the CIA? Surely Sarah could have gotten them to help without having Casey, Chuck, and Morgan show their faces. Casey is unconscious and badly hurt--allowing for Chuck's moment of crisis--but when Chuck calls Sarah, she declines to answer. Why would she do that if she could easily explain what happened?
Score: 7.5/10