I'll make it so that she simply died due to using too many of her runes, and that the researchers intentionally blanked her memory. Honestly, the whole memory loss subplot I felt was just a cheap excuse for the writer to add in melodrama to the whole Shouko betrayal thing, when it really wasn't needed, and just made Shouko come off as far less likable.
Yeah, the Council having their own mercenary task force I think makes them far more dangerous, plus it would also make it so that they don't get so easily wiped out at the end. Heck, I don't mean to come across as twisted, but one scene I have planned is that, in the aftermath of the massacre, the Taurus Company troops basically burn all of the bodies of the dead students and ARUS soldiers. One of whom happens to be Marie's body, as the heroes weren't able to hold a proper burial for her when they got back with everything that was going on. Both Haruto and Shouko see this as they are escaping, and it only adds to the guilt.
On a related note, I feel old too. Heck, it was me going back to the show after a decade that led me to do this, as I feel that there was so much potential that was sadly wasted. So, here I am, trying my best to fix it. Even if a lot of my personal fixes also involve relationships and the like in the show.
Btw, thanks for replying. Want me to give a few ideas I have for it? Personally, I'm most eager to get into the scenes between Haruto and Saki such as the former's rescue of her, and not just because of shipping, though that is a part of it.