Begin by thinking about how the two universes will interact. Will it be a full - on crossover where characters are constantly interacting, or more of a side - by - side story? Decide on your main conflict or goal for the story. It could be as simple as a friendship developing between a duck and a pony, or as complex as saving both worlds from a great evil. Then just start writing down your ideas, don't worry too much about grammar at first, just get the story flowing.