Complex sentence: Apparently, their attitude and further development over the story reflects that it was not their influence on the other Cylon models what led them to attack, but is revealed that this was the Cavils' purpose all along.
Split into simpler sentences: Apparently, their attitude and further development over the course of the story reflects that it was not their influence on the other Cylon models that led them to attack. Rather, it is revealed that this was the Cavils' purpose all along.