I have developed a game engine in c/c++ and DirectX.

I have a tile engine for the maps, animated player/npc sprites, talking to the npc, menus, and level changing but there is no game, it just feels empty.

I have looked around and keep hearing buzzword answers but I want to know how to implement a story in my game.

Some people have said a save file that holds flags governing every possible action/state available in the game but this sounds ludicrous.

It is a bit ambitious but I am aiming to get a game like the older Pokemon/Final Fantasy games.

Does any one know how these games work or the theory used?

I have been looking for a while and would really appreciate any input people have.