I generally come up with an outline of a plot in my head and then I get an idea of the characters along with it as well as their roles and how their roles compliment or clash with other characters. From there, I get ideas and develop everything more without writing it down and eventually I know everything about the characters by heart.
The first part and the ending are always the easiest for me to come up with, it’s the rest in the middle that normally leaves me wondering what should happen.
But for specific dialogues and specific scenes that pop into my head, I write them down. Usually they’re important dialogues and important scenes, or aesthetic scenes, touching scenes or scenes that really show character development for either one character, or more than one. For branching though, I put that into a table as I go along with writing, just so I’m not left wondering what my flags were named etc.