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Once the heroes reach the throne room inside the World of Nil, they come across Elgo who reveals himself to have been the Emperor of Avalon all along. He harnesses the power of Nil to become immortal, but after the party defeats him, he is consumed by the power and turned into the monstrosity that is Chaos Elgo.
The creature escapes between worlds through a dimensional portal with the heroes in pursuit. They face off with Chaos Elgo in the final battle, ultimately defeating him and saving the world.
The battle starts off with Chaos Elgo using Grand Wall, which deals roughly 3,000 physical damage to a single party member. It will also use Eclipse to deal about 1,000 damage to the party and randomly add Curse and even Gradual Petrify. Sometimes Chaos Elgo will counter with Gravity. After dealing a sufficient amount of damage, Chaos Elgo will transform into its Dark form and cast Dark Flow, instantly putting the party in critical state. After a short cutscene plays, the heroes will be revived with their buffs intact (and remove any possible status ailment). It is possible for Chaos Elgo to cast Black Hole, nullifying the status buffs.
From this point on, Chaos Elgo will switch between three forms: the default form which uses physical and non-elemental attacks, the Dark form which uses Black Magic, status ailments and Dark-elemental attacks, and the Light form which heals and casts buffs on itself while unleashing Holy-elemental damage. The light and dark forms are resistant to their respective elements and weak to the other. At this point his attacks for the Dark form involve Meteor, Dark Flow which now damage the party for 2000-3000 damage and heal himself for 4000, and Black Hole which dispels all buffs. For his Light form he can use White Form to buff himself with protective magic and heal himself for 5000, Pandora's Box which like the previous fight give him access to Axion, Neutrino and Neutralino and Holy, which can inflict close to 3000 damage and above. His normal form will use Eclipse, may counter attacks with Gravity and use high level spells.
Upon hitting half his HP, the boss will also use 10000 G's, which will reduce the entire party to single digit HP. When low on health, Chaos Elgo will begin to use Big Bang, which will deal around 4,500 damage to the party along with Sap.
Just like with regular Elgo, it is recommended the party be level 70 or above before attempting this battle. The battle will be long, so the player should ensure they have a good supply of Dry Ether and Elixir items. The Argy summon is helpful to counteract Chaos Elgo's Black Hole ability.
The party should begin by casting as many status buffs as possible, then unleash the strongest attacks available. Coming with two healers (preferably at least one Seer) one with Hermes' Sandals is of great help to guarantee keeping the healing up while the other healer buffs. Fusion Abilities like Mighty Wall, Hastega, Midareyuki, Final Heaven, Phantom Rush or Dance skill Sabre Dance all can be very helpful. The player should consider bringing a Paladin and a Dark Knight (or at least two people with their skill sets) due to Chaos Elgo's tendency to change forms thus making it viable to strike on his weakness point. If using the aforementioned jobs, one should be careful with equipping Light or Dark based equipment as they can heal Chaos Elgo in the wrong form, so using neutral equipment (or changing it through the item command) is a good alternative. Strike and Smash can both hit for solid damage, specially if buffed so that regardless of form, neither attacker is imperiled, otherwise the player can also use magical attacks like Comet, Flare, Meteor, Ultima or Bahamut all of which can deal high damage without worrying about elemental properties. Otherwise Dark Star and Holy are good ideas that can deal several thousands of damage to Chaos Elgo.
If Chaos Elgo casts Black Hole and nullifies the party's buffs, it is recommended to recast Shell and Haste as a priority. Hermes' Sandals cannot be dispelled so if equipped on the healer the player will have an advantage. If Chaos Elgo buffs himself with White Hole the Seer should be able to Dispel it as his defenses can drag the battle out longer than necessary. The player should always make sure a healer is ready to cast Curaga or Summon Argy or buff as Chaos Elgo will reduce the party's HP to single digits with 10000 G's which can be fatal if not healed quick and even worse if not buffed as he will likely follow with his strongest, Big Bang whose damage output can likely destroy an unhealed party. If possible Full Cure is an alternative to quickly revert this situation.
Overall the battle is basically a longer version of the previous, with more tricky moves involves. The tactics used on the last battle should work here as well, and the player is only advised to be more careful to evade being wiped out by Chaos Elgo's attacks, gearing the difficulty of the battle on its longevity.
The song that plays during the battle with Chaos Elgo is titled "Inside the Swirl of Chaos" and was composed by Naoshi Mizuta.