Four people were involved in the script for this episode, and that's usually not a good sign. I'm still not sure whether or not it was a good thing for this episode. While everything came together by the end of the hour, I was a bit surprised at how disconnected it felt from the previous episode. The only thing that seemed to bridge the gap was Olivia's abduction.
Olivia and Agent Broyles both find their methods and choices questioned in this episode. In this situation, it's treated as an unfair assessment of Olivia and her team. Objectively speaking, it's absolutely justified. Her team is unique, to say the least, and her own mental stability has been questionable. One can't even be sure her memories are her own. That's completely ignored, despite having been a major part of the previous episode.
Olivia's abduction is ultimately related to an odd scheme to take out doctors working on a task force for the CDC using super-sized common cold virus cells. All well and good, but how is extracting fluid out of Olivia's spine saving her from anything? It doesn't quite make sense at this point. The only thing to get out of it is what was already suspected: at least two sides are fighting for control of the product of The Pattern.
One side would logically be Massive Dynamic. Mr. Jones could represent the other side. As noted in the review for the previous episode, Olivia looks to be caught in the middle. Broyles looks to be in the tank for Nina Sharp at this point, so my suspicion is that Massive Dynamic is actually going to be the wrong side of this little war. Perhaps that explains why we haven't seen William Bell; maybe he's "disappeared from public view" because he's left the company and started working against them.
But those connections were only made, or in actually merely suggested, at the very end of the episode. Almost nothing else felt connected to the previous episode. Considering the long winter hiatus, that's a dangerous proposition. While I understand that the producers want to avoid an overly serialized format, keeping things cohesive is an important consideration.