The way the writers handled the plot was impressive, considering how dumb the ending of last week's ending was. They managed to bring everything together, resolving Morgan's Intersect problem, creating an explanation for it, and ending the episode on a solid, if implausible, cliffhanger. That and the hilarious subplot where Awesome brings Jeff back to normalcy were enough to make the episode enjoyable.
However, the character stuff with Morgan didn't work. We're supposed to believe that Morgan acted the way he did in part because he was a little douchey himself, not just because the modified Intersect made him that way. This is problematic, because there aren't any well-defined lines on how the Intersect works on his brain. When the Intersect kick in and take over Morgan? The hazy ideas behind how the Intersect works makes the character development also hazy, as we don't know anything concrete.
As an aside, Chuck's ratings have been horrible, even for NBC standards. Do not expect a save like in previous years.