Oo~ I didn't think of that! How about making those going into the experiments now not being the first wave to do so, and instead having those who went through it before that "defected" become a resistance- and the two factions of government being that like in Overwatch: Overwatch being the shining face of it all while Blackwatch did all the behind the scenes work. Ok I am actually really loving this more holy crap.
Ok sweet I'm gonna go back and re-edit the original post to add a few more ideas!