Just tried to play around with flags and SWEET HOLY SHIT this code is a mess. There are HUNDREDS of variables. Several seem to serve no purpose except to CREATE dependency. I don't know if Andrealphus still reads here, but dear lord identify what is NEEDED to make a program run. It saves you time on edits, additions, or error checking in future versions.
The only, and I mean ONLY reason to do this many interlocked variables is if you are 1) trying to break your own program 2) Make it so no-one can edit any values.
Better utilization of the integer checking that is done to create a progressive state instead of multiple independent variables (almost all events are linear, could set aside independent variables for the few lateral events). Or a python list (Renpy wonky version of arrays) would reduce the clutter significantly and allow for independent manipulation. Removal of several of these entirely would be sound.
I'm used to people "obfuscating" by naming things nonsense, layering indents, and doing other nonsense. I'm used to intro level code with dozens of if statements, switches, or multiple functions where only one is needed, but this is just... Like someone not only built a house log cabin style, but did it with matchsticks.