This episode felt unfinished. When Olivia and Peter are at the gas station Olivia says that the case is over, but its not. That "hive" of people from that IVF sperm donor is still out there.
But when we see Olivia kidnapped together with Nina Sharp it looks like the writers moved on to something completely different, namely the new shapeshifters. Nina Sharp could have been kidnapped months ago and been replaced since than with a shapeshifter. That would explain why she has been injecting Olivia with Cortexiphan.