In Final Fantasy XI, the storyline revolves primarily around missions through the governing nations that exist in the base game as well as each expansion that the player is affiliated with. Nation or governing body affiliation is quite simple, often requiring mandatory quests being completed and have many stages of progression to achieve higher recognition and reward throughout each story. Some missions are even required to be completed to further progress into the start of the additional storylines of each expansion or particular areas.
Players begin the game as residents of one of the 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 unveils 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 preventing their plans.
Final Fantasy XI: Chains of Promathia revolves around a Elvaan girl named Prishe and the dead Twilight God Promathia, who had originally cursed the Zilart race, and the attempts of various groups to either complete or stop his resurrection. The Wyrmking Bahamut is involved in these events, and wants to destroy Vana’diel to stop Promathia from absorbing the life of the world.
Final Fantasy XI: Treasures of Aht Urhgan concerns the Empire of Aht Urhgan which opens up to the nations of midlands after years of self-imposed isolation. 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 involved in the schemes of the Empress’s court and the growing fears of war and darkness coming to Aht Urhgan.