So I had another thought for plot.
There could be cells that splinter off from the Resistance and act without authorization, becoming more and more violent and terroristic. (I don't think we should shy from the fact that the game's protagonists are, technically, terrorists, but there are terrorists and there are terrorists.)
It's not that much of a problem at first, because the media will villify the Resistance with blatant lies to begin with, but as the game progresses, and the Resistance becomes more popular, the media begins to play up the acts of these splinter cells (ahem), forcing the Resistance to deal with them. i.e., the Silencer is sent to destroy them.