Physical attacks will cause Omniscient to cast Return, resetting the battle. The player can prevent him from casting anything by attacking him with a weapon enchanted with Silence. When Omniscient is defeated, he casts Flare as a final attack.
An efficient method to defeat Omniscient is to summonCarbuncle, so Omniscient's spells are reflected back at him. Another method is to cast Berserk on him and then summon Golem. This way, he cannot use Return to restart the battle, and the party will not suffer damage from his physical attacks. Provided the party is under Reflect, or Omniscient is berserked or silenced, Omniscient's final attack should not pose a threat.