The game that always comes to mind with this is Chris Avellone et al’s underrated masterpiece, Knights of The Old Republic 2.
Yes, I know it was released incomplete and buggy for a whole list of reasons, some of them due to Obsidian’s ambition and some down to the publisher, but that doesn’t matter.
So here’s the short version of the story: the folks at Obsidian got the contract to make the sequel to one of the biggest games in one of (if not the) largest multi-media franchises of all time. Knights of the Old Republic was Bioware at their best, and it was a tremendous success. Obsidian got the nod to make the follow-up.
Avellone went out and consumed pretty much the entirety of the existing Star Wars Expanded Universe as existed at that time to learn the territory he was going to be playing in. He did his research.
And he decided that, basically, the Star Wars universe was full of shit. That the entire notion of the Force as depicted in film and novel was self-contradictory, that the Jedi Knights were in no way the unambiguous force for good that they were commonly accepted as being. That there were multiple interpretations of how the Force was even supposed to work, and they completely contradicted each other, and yet they all worked.
So he made a Star Wars game about how Star Wars was stupid, and he wasn’t even done. He managed to attack and deconstruct and evaluate a huge number of the tropes of Role Playing Games themselves, especially ones like Bioware made with simplistic sliding morality scales. The game attacks the entire idea of gaining experience points from combat by making both one of the main villains and the player character
into walking black holes of life force, all consuming voids that destroy everything they come near. It gives you an elderly mentor character, the first NPC you meet, and she spends the entire game lying to you. Not obviously lying, but subtly and intelligently twisting the PC and the player’s interpretation of everything that happens. One who dislikes the player more if they uncritically accept what she says.
I could probably write an entire essay about the ways in which KOTOR2 is a masterpiece of deconstruction, but to this day, and every time I play it, I’m still in awe of the sheer audacity. How did they possibly get it past Lucasarts?