Renpy development is very geared towards making visual novels. You could make it do other things, but it is very much not designed for that, I saw someone make minesweeper in it once. But if you do use it for visual novel type things, it handles 99% of it for you.
As for the overarching plot, there is definitely one of those. There are even already bits and pieces of it hiding around. Perhaps try investigating the forest very, very thoroughly? In the end all things will be explained, although whether those explanations are clear is another question.