Cloud: I couldn't finish 'em. Looks like this's gonna get complicated.
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The Emperor boss, also known as the Empire, is fought twice in Final Fantasy II. The first encounter takes place at the climax of the party's invasion of the Emperor's Cyclone fortress, where he will be accompanied by two Royal Guards and one Wood Golem.
The battle is simple, since the Emperor is only slightly more powerful than his cohorts, whom the party has been fighting regularly up to that point. The party should defeat the extra foes first (since the Emperor cannot be attacked directly while they are alive), and attack the Wood Golem with Fire-element abilities. The Emperor will attempt to strengthen himself, along with his guardians with Blink 8 and Haste 6, but the difference will be negligible. His level 10 Thunder spell can be a nuisance, but otherwise the Emperor is not much of a threat.
The Emperor can use an Elixir to restore himself to full HP and MP, and he can use it at any point, even if he has high levels of both. One can abuse this by using Thunder-resistant equipment and Magic Defense buffs to render the Emperor's attack useless, and use his high HP and low offensive powers to train the Magic of the party, as with 3000 and Elixir, he can last for a decent amount of time to level up plenty of spells and stats by the time he is defeated.