Like CHAOS in Final Fantasy, the Emperor is designed not to make things easy on you. He has a whopping 10,000 HP, 210 defense, and resists all 8 Elements. He also has enough magic resistance that even non-elemental Spells will rarely gain any successes. What he does not have is a lot of evasion. With so many HP, the Blood Sword is extremely powerful (draining 625 HP per hit!), but Berserk and the Masamune and Excalibur work well too. Haste, perhaps cast from the Masamune itself, is also a great boon. Flare and Holy work in a pinch, but don't expect spectacular damage.
Unfortunately for you, the Emperor has a Blood Sword effect of his own. His 8 attacks have 180 Power each, but their ability to drain HP is the real threat. If Leon or another Character in the front row has insufficient Evasion, the Emperor might just use them to to heal himself.
The Emperor will only make basic attacks attack 30% of the time, but his other options are mostly bad news as well. Flare 16 will hit one Character for significant damage. Starfall 10 is even worse, dealing several hundred damage per Character, and Slow 16 can shut down a Character's physical offense entirely. Immediately counter by (re-)applying Haste, possibly with the Masamune. Curse and Blind should be Esuna'd as necessary. (Since none of the Status Ailments the Emperor inflicts affect mages, you may want to give Ribbons to your front-line if they don't already resist those effects.) The best case scenario is that he uses the bugged Dispel and wastes a turn.
10,000 HP is a large number, but keep at it and you should win eventually. When the Emperor falls, the ending will begin, and the game is over. Congratulations! You finished one of the hardest* Final Fantasy games. (*The "difficulty" is mostly found in dealing with FFII's nonsense, undocumented mechanics.)