Another way branches are used is to incorporate different fan theories. For example, there could be a branch that plays on the theory that Batman has some sort of metahuman ability that he's kept hidden. In this branch, Wonder Woman discovers this ability during a mission and it changes the dynamic of their relationship and how they approach future challenges.
Branches are often used to add variety and depth to the fanfic. They can create different scenarios and outcomes. For instance, a branch might lead to a different ending for a story arc. If in one branch Batman and Wonder Woman defeat the villain through combat, in another they might use their wits and detective skills to outsmart the foe.