Well, you just assume that they all die. Saria gets taken by the enemies in the Forest Temple and killed (thats my best guess). Darunia goes inside Volvagia's room to destroy him but gets killed instead. Ruto gets killed as well possibly. Impa goes inside the Well to seal Bongo Bongo again and gets killed by him. Nabooru gets sucked into the sand by Twinrova.

Now those are all just guesses on how some of them die...but a couple could be true...like Darunia.