That title is a curious contradiction (if the sun really is golden, how can the dawn be dark?) and there's another that lies at the heart of Golden Sun. It seems creators Hiroyuki and Shugo Takahashi can't make their minds up whether the magical force of Alchemy – which either binds the world of Weyard together, is responsible for its current state, or perhaps both – is a bad or a good thing.
The first game's central quest tasked players with preventing two characters from releasing Alchemy into the world. In a neat twist, the sequel saw you controlling one of the first game's antagonists, who discovers that its release would benefit the world. Yet the arrival of the Golden Sun is ultimately responsible for the destruction of certain parts of Weyard, for which the heroes of the first two games are widely resented. Everywhere, that is, except in their home town of Vale, despite said hamlet being all but destroyed in the process.
In summary: no idea.