Players begin the game as residents of one of these three main countries, San d’Oria, Bastok and Windurst, and must help band the nations together against the resurrected Shadow Lord.

The expansion Rise of the Zilart reveals that the Crystal War and the resurrection of the Shadow Lord had been masterminded by the Zilart princes Eald’Narche and Kam’lanaut, who survived the extinction of their race. The two Zilarts plan to become Gods by opening the path to paradise, and the player is charged with thwarting their plans.

Chains of Promathia revolves around the dead Twilight God Promathia, who had originally cursed the Zilart race, and the attempts of various factions to either complete or stop his resurrection. The wyrmking Bahamut is involved in these events, and intends to destroy Vana’diel to prevent Promathia from absorbing the life of the world.

Treasures of Aht Urhgan concerns the Empire of Aht Urhgan which opens up to the nations of Vana’diel. As a new and powerful nation, it is of concern to the nation of the player, who is sent as a representative. The player then becomes embroiled in the intrigues of the Empresses court, and the growing fears of war and darkness coming to Aht Urhgan.

Wings of the Goddess primarily occurs in the era of the Crystal War, 20 years in the past from the main Final Fantasy XI setting. Players discover and cross mysterious time portals, and are led to help the Regal Feline Cait Sith reduce the suffering of the era. The Wings of the Goddess storyline is still ongoing as of 2008.