The main character is male, 16, who can see floating cities in the sky. Mother and father, nobleman and woman, send him to therapy but this doesn’t help. He befriends a servant girl, 15, of the parents who can see the floating cities. They run away as the mother and father want to kill the girl as they think she is encouraging the boy and investigate the floating cities. Are captured by soldiers and brought into the palace through a tunnel system. Are told that the people on the floating cities are enemies and that anyone who can see the cities is descendant from the people on them. They are told to choose between being killed or becoming assassins to destroy the cities.
The cities are full of mages who had been cast out by the people of the world thousand of years ago. They had been chased down and the people had tried to kill them off. They used their magic to take away the mountains and make them float. Each city has a different precious stone (sapphire, ruby, diamond, emerald etc) in the middle that holds the magic that keeps the cities floating. They also have cloaking magic in them so only mages can see the cities.
This is a very rough story line that hasn't been worked on at all since it popped into my head. I'll post a more detailed one later. Hope you like the idea.