Remember that dissonance will manifest whenever any part of the game fails to align with the player's experience and expectations; this means the game systems themselves need to avoid clashing with each other, and also with the story materials. For instance, if you have a fantasy game in which an ancient sword of great power is a key plot device in the story, players will experience dissonance (or at least grumpiness) when acquiring the sword does not give them a new weapon! Avoid this, where necessary, either by making the plot device something the player can carry but not use (e.g. an orb only a sorcerer can use, but the player character is a warrior), or by adding a limitation to the weapon such that despite its power, the player can use it only sparingly (for instance, because it drains their life force while they are wielding it).
We generally fail to recognise that our engagement with most game systems is in itself a story-generating activity, because all game systems are representative i.e. they ask that we imagine some specific arrangement. It is precisely because games are inherently representative that we make the mistake of thinking there is an unavoidable clash between stories and games - but we mean by 'story' here 'a story in the style of a movie or TV show' i.e. a screenplay. The problem is not and never has been an insuperable gap between games and stories, it is that the stories created by screenplays diverge dramatically from the stories that game systems produce on their own. Sometimes this tension is felt as rupture (the imagined experience collapses), sometimes as inelegance (Hocking's complaint about Bioshock is more of this kind), but in all cases it is game dissonance.