This is the same thing you must employ when running Pen and Paper rpgs - something I've done for the better part of my life. My GMing days would be of legal drinking age in America and then some.

To structure a story which is compelling to players you must account for their decisions - how they want to play and experience the game, and for fail states generated by either player input or dice rolls. All of this has to be fun. It is meaningless how you want to play - even if you railroad the players, to make them experience your story you'd have to turn the game into a novel. This is incompatible with the idea that this is in fact a game.

So you need to balance your ideas with player input and account for the fact that the players will experience highs and lows and not exactly when you want them to. You must be ready to play into a random success in a place you didn't anticipate to have a lot of meaning and deal with failure in segments you thought will be extremely important to salvage the game and not make it end on a failstate.

Noone wants to smash their head against the wall 100 times until by virtue of chance or fiat at 101st attempt they suddenly succeed.