Prior to the battle
Following the Battle of Lindblum, Alexandria controls the Mist Continent. No longer needing her "weapons dealer," Kuja, who has left the Mist Continent for the Iifa Tree, Queen Brahne sets to destroy him and achieve undisputed world domination. As airships require Mist for fuel, Alexandria must rely on its navy to reach the Outer Continent. They set sail from occupied Lindblum where they force Lindblum's soldiers to help prepare the ships.
Regent Cid of Lindblum has his own plan to beat Kuja. Hoping his defeat would cut off Queen Brahne's magic supply and change the balance of power, he sends Zidane Tribal's party to deal with Kuja. Once Kuja is killed, he plans to use Lindblum's superior army to expel the Alexandrian occupiers from his country.
Queen Brahne commands the Alexandrian navy, and strikes with both cannon fire and a single spell made from the energy of all of her black mages. An attrition battle ensues, in which the Alexandrians run out of ammunition while fighting Kuja's monsters, suffering casualties and damages to their ships.
Watching from the Iifa Tree, most of Zidane's party is excited to see either Kuja or Brahne be destroyed. Remembering Brahne for the good mother she was before she came under Kuja's bad influence, Princess Garnet wants to save her, and attempts to summon an eidolon to come to her aid. She only manages to find Leviathan, whose Tsunami attack is deemed ineffective against airborne monsters, and dangerous to the navy fleet, and the summoning is cancelled.
By now losing, some Alexandrian soldiers want to pull out to avoid the destruction of their navy. Brahne is not ready to give up, and summons Bahamut, who lightly wounds Kuja. For a moment, Garnet is relieved, believing Bahamut will defeat Kuja. However, he uses the ancient airship the Invincible to possess Bahamut and turn it against its summoner. Bahamut destroys the Alexandrian navy with its Mega Flare, mortally wounding Brahne.
Brahne washes ashore on a nearby beach, where she is comforted by Garnet. Now free from the greed that possessed her, Brahne returns to her former self and asks Garnet for forgiveness for all the death and suffering she had caused. With her dying breath, she tells Garnet she will be a better queen than she ever was.
Although Queen Brahne was ruthless at the end of her reign, her legacy among the populace in Alexandria is built on her reign as a whole and she is remembered as a good queen, and Alexandria mourns for her passing.