Emperor Mateus in Final Fantasy II. When you finally face the Big Bad in 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.
Minwu and the other fallen heroes also get one when they refuse to be persuaded by the "reformed" Emperor and refuse his offer of immortality.
Josef holds off a boulder trap so Firion, Maria, and Guy can escape.
Minwu gives his life to unseal the ultimate magic, Ultima.
Ricard Highwind holds off the Emperor, having risen from Hell, while the others escape on the Wyvern. He stands against the ruler of Hell without any hesitation.
The opening FMV from the Origins remake deserves a mention, especially when Firion briefly disables a Black Knight with a pair of throwing knives. The first in its eye, the second in its throat. And it still gets back up, but it was enough to let Leon rejoin the group and for all of them to get out of Fynn.
Given how hardthe game is and all the Stat Grinding that must be fulfilled to be strong enough for the finale, beating it is an awesome moment for the player.
from the Origins remake deserves a mention, especially when Firion briefly disables a Black Knight with a pair of throwing knives. The first in its eye, the second in its throat. And it still gets back up, but it was enough to let Leon rejoin the group and for all of them to get out of Fynn.