The Troupe's airship, Prima Vista, is attacked by the royal guards, and damaged during the escape; it crashes in the Evil Forest, prompting Zidane to continue the trek to Lindblum without the rest of Tantalus. Zidane and Garnet are accompanied by Vivi and Steiner, who became entangled with Tantalus during their escape from Alexandria.
During their journey, Garnet adopts the alias "Dagger" and struggles to mingle with the locals. The group learns of a factory that is manufacturing soulless Black Mage warriors for Alexandria's use. Three powerful ones called Black Waltzes are sent by Brahne to retrieve Garnet by force, but in vain. In Lindblum, Zidane meets Freya and joins in Lindblum's Festival of the Hunt. Regent Cid has been turned into a bug-like oglop by his wife Hilda, for his womanizing behavior. Wishing to protect Garnet from Brahne's newfound aggression, he had ordered Tantalus to kidnap her. When the group learns that Alexandria has invaded Burmecia, Freya investigates the situation with Zidane and Vivi, while Dagger and Steiner head to Alexandria to ask Brahne to stop the war. Both parties are powerless to stop her, and Dagger has her eidolons forcibly extracted from her body. Brahne uses Dagger's eidolons to destroy Cleyra, after which she attacks Lindblum, forcing Cid to surrender. Zidane, Freya, and Vivi, after witnessing the assault on Cleyra, rescue Dagger, befriend General Beatrix, and return to Lindblum.
Afterward, Cid tells the party about Brahne's arms dealer, Kuja. The party travels to the Outer Continent, the location of Kuja's headquarters, through an underground tunnel with the help of Quina. There, the party meets a young summoner named Eiko, who assumes herself to be the last survivor of Madain Sari. They also discover a village inhabited by self-aware Black Mages. Their pursuit of Kuja leads them to the nearby Iifa Tree, an entity that emits fighting-stimulant Mist. They also learn that Kuja uses Mist to create the Black Mages. The party defeats the Iifa Tree's core and stops the Mist from flowing. When the party returns to Madain Sari, they confront Amarant, who was hired by Brahne to apprehend Dagger. Dagger slowly realizes that she is also a Summoner from Madain Sari. Amarant joins the party for his own reasons. At the Iifa Tree, Brahne turns against Kuja and intends to kill him with the eidolon Bahamut.
Final Fantasy IX takes place primarily on the four continents of a world named Gaia Most of Gaia's population resides on the Mist Continent, named so because the entire continent is blanketed in thick mist. Lands outside the Mist Continent — the Outer, Lost and Forgotten continents — are uncharted territories not explored until midway through the game. Several locations on the parallel world of Terra and the dream land of Memoria round out the game's areas. The Mist Continent features four factions: Alexandria, Lindblum, Burmecia, and Cleyra. Each country is separated by mountain ranges; the isolated Cleyran civilization, nestled in a giant tree in the desert, is protected by a sandstorm summoned by the village elders.Gaia is inhabited by humans and various non-human races. Alexandria and Lindblum are both populated by a mix of humans and anthropomorphic animals.