Actually, it was the same with Sephiroth. He was mostly confused; (SPOILER) even to the point where he himself thought that he was part of the Cetra - the Ancients. He thought at that point that the planet belonged to his race and only his race, or something bizarre and twisted like that. So in some ways Kuja and Sephiroth are similar.
Though to be honest, FFVIII and FFIX have this one problem in common: (SPOILER)the final bosses of both games just suddenly appeared out of the blue.
