The concept of the "flying dungeon" is all about adapting your plot to fit the actions of the characters. One of the issues we addressed is that giving players Freedom to make whatever choices suit their characters can run contrary to Fun if they go so far off script that you don't have anything interesting for them to interact with. Realistic as that is, it's not why we're here.
The "flying dungeon" moves its elements around behind the scenes, so that no matter which way the PCs turn, or which door they go through, they'll stumble across at least some pre-planned element that will be fun to interact with and give them something to do. Since the PCs have no way of knowing what was behind that door before they opened it, all the flying elements of the Flying Dungeon move, invisibly, behind the scenes.
The natural problem with the flying dungeon is that it creates a sense )at least for the SH) that the choices the PCs make don't matter (whichever way they go, they enter the same room), which is why it should only be used as a last resort. Plan as much as you can for the choices you can expect the players to make. Use the flying dungeon model only when they go deeply off the beaten path, to the point where there's no longer anything interesting for them to interact with at all. The dungeon, or at least parts of it, fly to them.
Despite the name, the flying dungeon is more often uses with pieces than places. Flying enemies move to create opposition along whatever path the PCs take. Flying treasure makes sure they get rewarded for their efforts, even if they went left instead of right. And flying clues (maybe the most vital) ensures that they have enough information to keep moving forward in pursuit of the big picture, regardless of which path they took or whether or not they decided to loot the Goblins they just fought.
Again, flying elements should be the exception, not the standard, but it's a good concept to have in mind to ensure the PCs still have fun while simultaneously allowing them to be their unique, quirky selves.
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