I think the best way to subvert expectations is shock value, just like in the real world all books/games/shows have common rules too.
For example, if a character talks about their Hope's and dreams for the future and all these plans of things they want to do at some point in time, that character has a 90% chance that there going to die, 95% chance they'll turn evil. Hell having that character not do either would be more surprising.
For me, I'm not going to kill myself making one huge plot that's suppose to deceive the player cuz the players going to have 2 or 3 options in their head of how the story will.play out, I rather pick small moments In the story to absolutely flip things with shock value, let me explain a bit.
Let's look at how tragedy is dealt in stories: Death, in today's mediums you can almost always find death of a main or supporting character being the BIG MOMENT in the story, the bad guy or one of his men kills your best friends cousins mom. Horrible, just horrible, but come on its expected, but theres more than one way to tackle tragedy isnt there?
What if the bad guy didnt kill your best friends cousins mom? What if instead he/she kidnapped her and tortured her gruesomely by ripping off nails and burning off her hair, or what if the bad guy broke her spine leaving her confined to a wheel chair?
What if the bad guy is a pervert and after he defeats your entire party, he captures the Male and female members of your party, but when you go to save them you find out the bad guy sexually assaulted BOTH the male and female because bad guy is bisexual
The problem with this method is it's easy, ESPECIALLY with rpg maker, for this to come off as tacky and tasteless when done without lots of planning, but if done artistically and with the proper world setting things like this which are not the norm are what make players/readers/watchers go nuts.
Theres not a single FF7 fan who doesn't love sneaking into the Don's mansion by dressing up as a woman &
I dont know a single game of thrones fan who doesn't dry heave in self satisfaction when you mention the words "red wedding" to them. These moments are not the norm and were nowhere near the viewers expectations the first go around.