Emperor Mateus in Final Fantasy II. When you finally face the Big Bad on his throne room, the boss fight is depressingly easy. A good party ends up killing him rather quickly. Then the Dark Knight steps forward, and you think that the Emperor was a Trick Boss, and that Dark Knight was the Man Behind the Man. But then the Emperor reappears on his throne, in a new monstrous form. Turns out that he died and went to Hell... and then took it over!
Then, of course, the party scores a collective moment when they literally go to Hell and back to beat the Emperor.
The Emperor didn't just take over Hell. His "light" side went to Heaven...and took over Heaven as well!
In the GBA and PSP remake, all the dead party members go to Heaven, and beat the light half of the Emperor! (Yup, the Emperor is so bad that even his GOOD side was evil!)
Minwu earns himself Ultima, the ultimate magic that he had died to unseal.