There are two endings to the main story, depending on a choice you make (torture or talking. Yes, I stole this from MGS).

The ending caused by being tortured:
After the final battle, Plaza picks up the main villain's hammer and prepares to finish him off, but he falls to the ground randomly. Bean walks in and notices that the main villain is recovering. The main villain then grabs Plaza and shoots some at him. This starts growing and the main villain fades away.

Turns out that this is stuff that the main villain is using to possess Plaza and use his body as a replacement body. Plaza then attacks Bean, the final boss of the game in this ending.

After Bean has been defeated, he falls over and is kicked off the tower, meaning he was probably killed. This unlocks the Evil second story, which focuses on hunting the other party members that helped you in the main story.

The ending if you told the main villain about everything:
After the final battle, Plaza grabs the main villain's hammer and kills him. Plaza hears a bomb about to explode and jumps off the top of the tower.

The player's rival, Leviathan, rescues him in a helicopter and lands on a field.
Leviathan then says "Congratulations on saving 3DSPlaza. However, I have some news for you; you won't be credited!"
A battle then starts. If you lose the battle, Bean will appear and another battle starts. If you lose this time,
you'll be back at the final boss.

There will be a second story for this ending too.

There will be more choices that change the story.