There was actually a whole subplot removed. There was supposedly a whole thing about a virus getting out and killing people. From what we know the virus was created by the Power Broker, who then controlled the only vaccines. The Flagsmashers went rogue stealing the vaccines from the Power Broker to give to those that couldn't afford the Power Broker's monopoly, and with the help of moles inside the US Government (Likely Val AKA Julia's character),the Power Broker created John Walker to stop them.
It's likely, considering the whole show also had a deep subplot about the nature of refugees and minority discrimination, they likely felt they were stacking a bit too many "controversial" topics on top of each other for a single show, so they dropped the vaccine plot and replaced most of those scenes with stolen super soldier serum instead, leaving a good chunk of the show feeling disjointed.