First you'll need to settle on the broader story structure. Narrative games - like visual novels - can take very different approaches when it comes to handling their branching paths. The most simple approach would be to have no branching paths at all, but once you include player choices, things become more complex. Here is a very good summary for the different structures that can be employed:
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The gameplay you envision will very much guide your choice of structure. If you for example want some lifesim like structure, with your main protagonist having to manage her daily life while struggling with all sorts of dangers, threats and corruption, then your narrative would be structured around some central hub. This would be some choice screen where the player decides on a daily activity the elf will attempt, and the resulting narrative branch will loop back to that central hub while raising and altering some central traits and variables, which might alter how the very same loop will play out in the future or unlock new options in the hub.
If you on the other hand picture a more straightforward narrative, then you might have a few branching paths (or just a single one with some bad ends and some purely aesthetic branching sections), which would be told much more closely to a traditional story.
Each approach will require a very different way of writing, so you and your team should settle on a gameplay loop first, before starting the writing.