First of all, MASSIVE SPOILERS AHEAD obviously.

Feel free to analyze this graph and suggest some fixes or updates (or just point out errors or ask for clarification). The graph was made with some assumptions (most of them are written at the bottom). It may not be exactly what you are looking for, but it makes sense for me. And I was making it for myself, because the only thing I could think of after finishing the game was that I needed answers. I spent many hours getting this thing to work somehow and minimizing plot holes and I can finally say that I understand it all (with sufficient margin of error) and I am free. I want to share my enlightenment, so here you go. I hope it helps. Have fun!

You may want to get the picture zoomed in somehow.