Fire rune:- Chapter 4, Defeat the Beguiler and his clown to get the rune.
Water rune:- Chapter 8, reunite the lost brothers to get the rune.
Dark rune:- Chapter 10, reunite the two children with their mother to get the rune
All you have to do is make them chase you into where the tiles form a medusa head.
Just do one gorgon, and then the other. and when they see each other, watch what happens.