Pretty much ends on a downer, no matter what choice you make (you get 2). You either choose to arm a nuke and wipe out everyone in Harran and the surrounding countryside (where The Following takes place), or you choose to keep going and you'll turn into a Volatile. Basically there is no hope for the infected. The people in the countryside thought they had found a cure but they just found a way to slow down the infection and they were slowly becoming pretty much like worker bees, controlled by the "mother".