The man in charge of the Zelda franchise has announced that the series' main antagonist, Ganon, won't be appearing in Zelda: The Skyward Sword at all. Instead, the antagonist will be a character called Lord Ghirahim.
"I wanted to make to make a character that contrasted what people think about Ganon"“someone who is a little bit mysterious," said Eiji Aonuma.
Aonuma also revealed that Skyward Sword will take place before Ocarina of Time and will explain the origins of the fabled Master Sword.
Source: Nintendo Charged