Prototype crossover idea.

For my newest story 'Bringing the World to its Knees' I have an idea on how I'm going to do this. The first two three chapters are going to be the constant chapters, and after that, I'm going to split the chapters down two different paths. One is going to be the main one, where he infects all of the ponies and possibly takes over the world, and the second, side story, is going to be what happens if he actually goes with the ponies. I thought about this idea, ran it by some people, and they approved of it.