I'd do it in an actual city, like repelling an enemy attack. I'd also have 3 core bosses spread out in different parts that can be done in any particular order, but upon clearing one, a dungeon wide effect comes into play (like reduced MP regen, a poison debuff, enemies get haste or resistance to non-magic damage).

So basically you have to kill the bosses in any order, with each having ups and downs depending on your group composition.

Upon clearing all bosses, the "big boss" arrives at the Aetherite Crystal area for the big showdown.

(Yes this is basically Dynamis from FF11)