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The Second Battle of the Iifa Tree (March 5, 1800) occurs shortly after Terra's fall, when the Lindblum fleet and Alexandrian royal airship, the Red Rose, intercept the numerous Silver Dragons swarming out of the strange orb of light above the Iifa Tree in order to clear a path for Zidane Tribal and the party as they intend to storm Memoria on board the Invincible.
Shortly after Kuja uses his newly acquired Trance powers, he learns from Garland's spirit that his power would never matter as he would die soon anyway; Zidane, the "Angel of Death" created after Kuja, was meant to replace him. Upon learning that his amassed power would soon go to waste, the enraged Trance Kuja destroys Terra. Zidane and his party manage to gather all the Genomes in the Terran town of Bran Bal, commandeer Kuja's airship, the Invincible, and narrowly escape back to Gaia.
Unfortunately, the Gaia they return to is not the same as before Zidane and crew traveled to Terra; The Iifa Tree had gone berserk and forced its roots to burst out of the ground on all four continents of Gaia, casting a worldwide layer of Mist, previously isolated to the Mist Continent. Mist-created monsters invade various points of the planet. More significantly, a portal to Memoria appears above the tree. Kuja intends to go through it to find the Crystal, the origin of all existence, and destroy it. His motive is that if he cannot remain immortal, no matter how much power he amasses, then neither can any other being.
Realizing this imminent threat, after leaving the Genomes in the care of the Black Mages in the Black Mage Village, Zidane and crew agree to themselves, on Garnet's behest, not to inform anyone of this danger, as well as their intention to invade Memoria to stop Kuja.
In their attempt to defeat Kuja within Memoria, the Invincible is attacked by swarms of Silver Dragons to prevent them from entering. One dragon is about to fire its breath at the Terran airship at point blank range, when it is suddenly obliterated. Looking behind them, Zidane and Dagger see the Lindblum fleet, under the command of Regent Cid IX, attacking the dragons. On board the flagship, the Hilda Garde III is the Tantalus Theater Troupe, present to cheer for Zidane.
The Invincible flies on while Cid's fleet keep the Silver Dragon occupied. However, one swarm is distracted by the ruse and follows the Invincible. The swarm would have attacked had not the Red Rose, under General Beatrix's command, suddenly burst from the Mist behind the Invincible, acting as a shield with Silver Dragons smashing into it.
With all the dragons dealt with, the Invincible is able to break through into Memoria. However, the Nova Dragon lay in waiting at the gates, and has to be felled by the party.
Once in Memoria, Zidane and company eventually traverse the dimension, fighting through the revived Shrine Guardians, now the Four Fiends, and Deathguise, while witnessing past memories (such as the destruction of Alexandria and Madain Sari) and seeing Gaia's past and origin. Eventually, they make it into the Crystal World and engage Kuja in one last battle.