The JJ said:
Quoting limited to 5 levels deep
By beating bosses which inturn would grant them an ability. (You could make it like a 100% deal.) Here's my idea.
You have to beat the main villain, yea. But each dungeon has an elder/spirit/goddess trapped in it. And when you defeat the boss, the elder/spirit/goddess is released. And in order to have 100%, you must beat all dungeons. Then, a second story pops up. You have to go through two more or so dungeons to reach the REAL bad guy who imprisoned the spirits and once you do, you win.