In Native, all stationary "parties" (things on the world map)--namely towns, villages, castles, and bridges--are visible to the player character (who is new to Calradia per the character creation story) from the start of the game. This doesn't make a whole lot of sense, so the "Fog of War" option will hide these towns, villages, castles and bridges until the player is close enough to see them on the horizon. Then, knowing where they are, they will remain visible for the remainder of the game (like they are from the beginning in Native).
Fog of War can be turned On (map locations hidden until visited) or Off (always visible, as in Native) both at character creation and from the Mod Options screen. (Give some in-game traveling time for the change to activate if altered from the Mod Options screen, however.)