I’m making a linear visual novel with partial interactivity that allows the player to influence small portions of the story, but I just want to know how one goes about drafting something like that. The interactivity feature allows you to build a relationship with some characters, this is what can change different parts of the story. Thing is that I have several other characters whose growth I would like to cover, but don’t know how.
When I read your question I see two different goals. 1 you want to make a rich and deep story, and 2 you want to include some slight interactivity elements to help build some of the characters relationships with the player. As such I think you should approach the two goals separately.
Here I would first write a full story with your characters. As the player is playing a limited role in how the story plays out just writing the plot and the interactions can help you define how each of the characters act and interact. In addition to this it can help to make a “Lore Bible” or a document where you record all sorts of information about the different characters. Their birthdays, what they like to eat and drink, who was their prom date, and various other life events. This can help keep your characters consistent and real.
You want to add some limited interactivity with the player. There are lots of ways to do this whether it just be keeping a bunch of boolean values that the player ticks off as the go through the story or by keeping various “relationship scores” on how much the player has interacted. To get this done you can create your own system in Java or C, or you could use a system in existence. Personally I’m a fan of Twine.
I should also note that this seems to be a good question for the writing stack exchange.