I'd say this turned out pretty well, the basics of it is Jetstorm's Decepticon coding takes over and he runs away and becomes a thieving 'con.
Meanwhile, Jetfire is a prime living a happy life, and keeping order.
Yet both think the other is dead.
Decepticon Storm theme song - Dead Inside by Skillet
Fire Prime theme song - Would It Matter by Skillet
Yes, the first chapters are neccesary for story telling reasons, there are ponies in other part.