Final Fantasy IX begins with the Tantalus crew, which includes the main character Zidane, flying to Alexandria on their Theater Ship, ostensibly to perform 'I Want to be Your Canary' but in reality to capture the Alexandrian princess, Garnet. This section of the game also introduces the playable characters Vivi, a young Black Mage, and Adelbert Steiner, the head of the Pluto Knights from Alexandria Castle. The Princess is apprehended, but during their escape attempt, Queen Brahne fires on the Theater Ship without regard for her daughter's safety, which results in the ship's crashing in the Evil Forest, south of Alexandria.

While escaping from the Evil Forest, Blank - a member of Tantalus - is turned to stone. From there, the party travels through the Ice Cavern, fighting a Black Waltz - a black mage that looks like Vivi - in the cavern. Once they exit the cavern, they travel to the village of Dali, where they discover a factory that is producing black mages like Vivi, as well as fight another Black Waltz. Garnet also decides to try and act less like a princess, adopting the false name Dagger. They hijack a cargo ship there, and fly it through the South Gate to Lindblum, defeating the last Black waltz on the way. In Lindblum, they discover it was Regent Cid, the city's ruler, who ordered Tantalus to kidnap Garnet because he was concerned about Queen Brahne's behavior. Cid's best Airship has also been stolen by his wife, who caught him cheating and used her magic to turn him into an oglop, a disgusting kind of bug. The party also participates in the Festival of the Hunt, where they meet Zidane's friend Freya.

   Back at Alexandria, Princess Garnet is being prepared for her coronation, following the death of her mother. Doctor Tot gives Dagger the stones that contain the powers Zorn and Thorn had extracted from her. Zidane, however, is bothered that Dagger is going to stop traveling with him, but he can't express himself. The party leaves Alexandria with Doctor Tot to attend a card tournament in Treno. The champion of the tournament turns out to be Regent Cid from Lindblum, who flew to Treno on his new, experimental airship. After the tournament, Eiko says that she heard from one of the Moogles that Alexandria was under attack.

The party flies to Alexandria in Cid's new airship, where Dagger is commanding the Knights of Pluto and Steiner and Beatrix are trying to clear the city streets of monsters. Kuja has summoned Bahamut to attack the city. When the party's airship is directly over the castle, Eiko jumps from the bow and floats down to a high platform where Dagger was waiting. Their combined summoner abilities, along with the four special jewels they possess together summon the Eidolon Alexander, who protects Alexandria with his wings. Kuja attempts to control Alexander the same way he controlled Bahamut, but his efforts are thwarted by a mysterious man named Garland.

GARNET

STEINER

QUINA

AMARANT