So I found that secret level above the living forest and fought Mileena but she ended up kidnapping Kitana.
Do I fight her again somewhere else or is she the only enemy that lives on?
If I recall correctly, she does get away. It's been awhile since I played. Have you done the fight with Mileena and Jade? If not, then you get to fight her again; if so, then she doesn't resurface.