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Missions are a special category of quests the player can undertake in Final Fantasy XI that are considered the main storyline. While optional, they differ from regular Quests in that Missions are sequential and are tied into the history and main storyline of the game and its expansions. They are very cutscene-intensive, and in the case of expansion packs, always encompass what each expansion is named after.

Many missions require the player to fight and may involve battlefields with unique Notorious Monsters. Others require the acquisition of a particular item, delivery, speaking to an NPC or even playing a minigame. Progress and completion of missions often unlock numerous benefits to the player, including access to new areas, increasing Rank, crucial features such as airships, and unique pieces of equipment among other things.

Missions are divided into several different campaigns. The original game has campaigns for the Republic of Bastok, the Kingdom of San d'Oria, and the Federation of Windurst each, which crisscross each other up to and including the final mission. Rise of the Zilart introduces its own campaign, and extends the three nations' campaigns in separate directions. Chains of Promathia, Treasures of Aht Urhgan, and Wings of the Goddess each feature their own campaigns as well.

Treasures of Aht Urhgan and Wings of the Goddess also feature a new type of non-story mission campaign. They are basically a series of tier-based repeatable quests that offer a variety of rewards and serve to flesh out the backstory for that particular expansion.

The various story add-ons each have their own campaign, whereas the battle add-ons have one storyline that spans all three add-ons. Because of the story for Abyssea, add-ons are not limited to a single add-on alone, they have been labeled as Quests instead.

Apart from the Rise of the Zilart missions, which require completion of the original storyline, all other campaigns are not dependent on progress in other missions. However, all campaigns are considered to be related, and links are often implied within the story. There are also a number of special quests that require completion in two storylines and directly link them together, such as Apocalypse Nigh.

Shown below are all the campaigns available in Final Fantasy XI:

Non-story missions