Fighting the dark queen (or whatever is her name, the one boss with the chains) you talk with Beatrice a few times and she doesn't go away and keeps fighting you until you die

If Beatrice doesn't go away on her own that means you have a weapon in your inventory that can hurt her. That weapon is Holy Sword. Equip it and off you go to a "good" ending.

Beatrice only goes away on her own if you can't beat her (you don't have Holy Sword) . In that case you get ending #2 which is considered a "bad" ending although storywise I don't find it bad at all.