The quests in The Burning Crusade are generally set in continuity with original lore quests, meaning that timeline speaking, BC is basically the direct sequel to the original WoW. Some quests set in Outland, especially those that are related to Illidan, do speak of a five-year hiatus in the storyline, which suggests a one-year long interval between BC and the original. This is however unconfirmed, since there never was any real statement that TFT takes place one year after RoC. But generally agreed, there was a four year break between Warcraft III and WoW.

The expansion is primarily based in Outland, the former world of Draenor and the new continent in the game. Quests generally allow players to explore the world on their own. The main story centers on Illidan the Betrayer and what happened to him during the last years. Players can also go on quests that suggest helping Illidan in his time-being or slaying him for a special reward.

Other than that, many links between the former world of Draenor and the current Outland are also made, such as the opening of the Dark Portal by Medivh, which is an instance quest located in Caverns of Time. Retelling of the old relationship between Orcish shamans and the Burning Legion is also told in quest-sequence storyline.

The Burning Crusade also centers on the two new playable races and their affiliation to the gameline. Many plotholes are filled with quests that set the blood elves in with the Horde and the draenei with the Alliance. Players still have to be part of the old world quests in order to obtain lore related to Outland.