In Fate, anything can be a character, so why not a map? When the threat is a map, your big bad has zones (page XX) which must be navigated to achieve victory.

As you detail your big bad map, each zone might have its own skills, aspects, and stress capacity. Some zones might contain simple challenges that must be overcome in order to move deeper into the creature. Each zone may take an action as a separate character against PCs occupying that zone, or in the case of a zone representing a limb or similar, may be able to attack adjacent zones as well. If a zone is taken out by one of the PC’s attacks, it may be bypassed and no longer gets to take actions of its own, but the overall big bad isn’t defeated until the heroes can reach its heart and kill it true.

This method works particularly well if your big bad is a truly gigantic monster, but need not be limited to that situation. You can use the idea of treating the threat as a collection of interconnected characters, without requiring that the PCs actually enter or navigate the big bad as a literal map. Used this way, you’ve got a hybrid between a map and expendable minion armor (page XX)—a hive of characters, after a fashion. Some parts of the big bad must be defeated before the players can hit where it is truly vulnerable, and those parts get to take their own actions in the exchange.

Whether you fully engage the map idea or simply build the big bad as a hive, you’re sure to end up with a more dynamic fight where the big bad acts more frequently, and the players must figure out a plan of attack that eliminates the threat piece by piece before they can finally put it down.