I had originally concocted this idea for the Forest dungeon, to have an event that sets the dungeon ablaze and then later burn out into a desert, but it was too... gimmicky.

Instead, why not apply it to the world map?
How about the world around the final dungeon is a rainforest at the start of the quest, with Giant trees blocking the entrance.
After completing the 'Simple' (First) dungeon, the forest catches on fire. Venturing further into the area would now be possible, but the final dungeon would still be blocked by burning trees. Also, it would give a chance to show off fog effects and underfoot damage combos (Can't breath very well in a burning forest!)
Finally, after beating the 'Gimmick' (Second) dungeon, the fires would burn out and the rainforest would be left as a burned-out wasteland. Access to the final dungeon would at last be possible, and it would look awesome in the process.

So the question is, can it be done? I'm sure somebody knows how.