The Battle of Alexandria (February 6, 1800) takes place in Alexandria soon after Garnet is crowned queen in Final Fantasy IX when Kuja returns with the intent of showcasing his newly acquired power to summon Bahamut.
Kuja summons Bahamut, which blasts the town with fireballs, destroying many buildings and setting their remains on fire. The Knights of Pluto are called before the new queen to deal with the situation, and she must select the right tasks for each knight.*Done correctly, this yields the player a reward. Two are ordered to gather information, two are sent to protect the citizens, two are ordered to prepare the cannons, and two are ordered to contact Lindblum and request reinforcements (the reinforcements, if ever sent, did not make it in time). Steiner and Beatrix work together to slay the hordes of Mistodons that infest the town, and have some success clearing the streets. An Alexandrian soldier confirms after the battle that the Knights of Pluto succeeded with the evacuation of civilians, and that Alexandria subsequently had few casualties.
Garnet stays in Alexandria Castle and hears a mysterious voice calling out to her. A previously inaccessible portion of the castle opens up when she investigates and Garnet climbs to the top of the structure, her pendant beginning to glow. Eiko, flying above Alexandria on Hilda Garde, hears the voice and knows what it means. She jumps off the ship to reunite with Garnet atop Alexandria Castle and explains to the bewildered queen the phenomenon that they can sense is the Summoner's Call—Alexander, the legendary eidolon, is calling for the pair.
Eiko and Garnet combine their magic by bringing the four crystal shards together and summon Alexander who spreads its gigantic angel wings to shield the castle and deflect Bahamut's energy blast. Alexander unleashes holy beams of energy that defeat Bahamut while Kuja watches on in fascination of its power.
Kuja repeats the tactic that won him the First Battle of the Iifa Tree and attempts to enslave Alexander using the Invincible. Opposed to Kuja's plan to control the eidolons, Garland intervenes and halts his plan.
Zidane's party rush to save Garnet. Upon reaching the top of the castle, Zidane - regretful that he didn't confess his feelings for Garnet earlier - insists on continuing alone, and tells the others to leave the castle before it is too late.
Garland uses the Invincible to destroy Alexander, along with the castle and most of Alexandria. As Alexander's wings wither and the castle begins to crumble, Zidane jumps down and grabs Garnet, with Eiko taking hold of the rope as well. They briefly share a tender moment where Zidane apologises for not being honest with Garnet, but have to evacuate as the castle comes apart. For the second time in 500 years, Alexandria is destroyed.
Zidane rescues Garnet and Eiko from the ensuing chaos and together, along with rest of the party, they escape on a ship stolen from the port, courtesy of Tantalus. They return to Lindblum where Zidane recovers from his injuries. Traumatized by both losing her mother and of being unable to protect her kingdom, Garnet blames herself and falls into despair, resulting in her losing her voice.
Alexandria sustains heavy damage, and the connection between the port and the city is blocked by debris. However, thanks to the evacuation Queen Garnet ordered, very few civilians lost their lives during the attack. The party can return to the city later and find its citizens busy in repair work, although much of the castle is no longer accessible. By the time Tantalus returns to the city to perform I Want To Be Your Canary Alexandria has recovered with the castle and town rebuilt to their former glory.
The attack on Alexandria shows Kuja's true colors to Garland, and from then on the two are enemies. This sets the stage for their final confrontation in Terra.