Wings of the Goddess did the story line differently. The main story missions were interspersed with quest lines specific to the 3 main nations of the Middle Lands -- Bastok, San d'Oria, and Windurst.
You would have to progress through the missions for a while, then the quests, then back to the missions.
In the game, the story isn't really broken up into distinct chapters like many of the other mission lines. I split it up into chapters based on major new developments in the story, sort of like acts in a movie.
Here are the quests for San d'Oria.
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