"You have braved the bowels of Hell to reach me. But the hand of man, which deals in false justice and forsaken love, can never hope to defeat the lord master of Hell!"
The battle with the Emperor is similar to most other Final Bosses in the Final Fantasy series. He is very powerful, dangerous, and attacks relentlessly, similar to the Light Emperor. His physical attacks also bear the same Drain effect that Astaroth had before him, meaning every hit he lands will replenish his HP supply. He will attempt to inflict a handful of status effects on the party to hamper their attack, including Blind, Slow and Curse. His offensive magic arsenal includes the powerful Flare XVI and Starfall X, which hits the whole party.
The party should equip the Blood Sword and make sure they are at full health. As the battle begins, the party should raise the magical barriers, including Blink, Protect, Shell and/or Wall, or use any items or weapons that will invoke any beneficial effects. Berserk and Haste cast on the melee characters bolsters their attacks. Ethers or Elixirs can be used to replenish the MP of the magic casters. It is important for the party to deal more damage to the Emperor than the amount of health he gains every turn. Maximum damage is the key.
Alternately, most of the party can swap to the back row, rendering the Emperor unable to attack them and thus unable to heal himself. Casting Blink and Protect on the front-row fighter will further help mitigate his healing. His spells do comparatively low damage, so bows and Holy/Flare can defeat him fairly quickly and safely.