Final Fantasy V: Third World
FF5 does something cool at the start of the third chapter. To recap: chapter 1 takes place on the planet where the supreme bad guy X-Death was imprisoned thirty years ago, and at its climax X-Death breaks free. Chapter 2 take place on X-Death’s homeworld, where you rush around getting Dawn Warriors killed and failing to stop X-Death’s master plan. But you do eventually face X-Death in battle and defeat him. Not that you expect this to stop him or anything. He’s been killed before, after all.
Immediately after this fight, everything goes dark, and the heroes find themselves lying on the ground near Reina’s castle, which is back on world 1. Except… things are different. The land is connected in ways that it wasn’t before. I didn’t understand what had happened at first, but I still got a sense that there was Something Very Wrong.
What happened is this: the two planets merged. The chapter 3 map is a melding of the chapter 1 and 2 maps, which fit together like a jigsaw when overlaid. An inaccessible mountainous island from world 1 is now in the middle of a bridge from world 2. A region where both worlds had an archipelago now has an uninterrupted land bridge.
It seems that the two worlds were once one, and that reuniting them was essential to unsealing the power of the Void, which X-Death wishes to claim for his own. Why does sealing the void involve splitting a world in two? Because the designers came up with this neat gimmick and needed an excuse to put it in the game.