The base theme of the game is that of war, over an age-old power: That of Magic. The plot is elementary in the beginning as it is the Gestahlian Empire versus the secretive freedom fighters, known as the Returners. It all gets hairier following the introduction of Terra; a half-Esper who was once controlled by the Empire, and once her true heritage is noted the real fight begins. his due to the return of the Espers, and Kefka's campaign to capture all of their Magicite for his own.
The setting is just that; a battle to save the Espers and the people of the World of Balance (Later World of Ruin, following the Empire's besiegement of the Espers.)