Identify whether the branching story is primarily for entertainment or instruction. Both instructional stories and entertaining stories should initially be plotted as two main points: the beginning of the story, and the resolution. Choose where the story or lesson will begin, and where it will end. Write this down.
Set a certain number of steps between the beginning of the story and the end. Branching stories generally need from 3 to 8 steps--at least--to be engaging.
Plot each step of the story chronologically. End each step with a choice that forces the reader to the next branch. In an instructional story, the steps may be paired with a multiple choice question segment, which will cause the story to loop backward if the recipient of the lesson provides an incorrect response.
Follow every permutation of the branches to check for any errors or inconsistencies. Make sure each branch of the branching story makes sense, and deposits the reader in the desired place.