Professor Tomoe and the Ayakashi Sisters died because their fates were changed by the anime and the game reset that.Some force reached out and changed their fates to differ in the anime. The general theme of the game is that one has to accept the past. In order to stop Apsu, all changes had to be reset.
Apsu is not as bad as she seems.Apsu. A shaman hell-bent on Screw Destiny? Or just unknowingly ruining people's lives and can't comprehend the repercussions of changing the past? Or worse, just desperately trying to survive due to the Silver Crystal slowly but surely killing her? The game does not explain why Apsu wants to change the past or why she wants the Silver Crystal...was it a roadblock to her plans or just her trying to survive? And what if Apsu is fleeing from other beings of her kind, probably wanted for changing other fates? Or worse, fleeing from her own fate? Gives a lot of good ideas for Sailor Moon: Another Story 2 doesn't it?