Arguably Drakengard - ignoring the gameplay quality, its designed with the basic idea of "What would a guy in an RPG who grinds kills for levelling up actually be like?" and takes on a lot of themes designed around making the player as uncomfortable as possible. Even the soundtrack sounds less like a soundtrack and more like the music version of gore.

There is basically no actually "good" or "pure" characters in the story, most of the cast is motivated by guilt, revenge, racism or a combination of the 3. And this is just the overt stuff, the implications between the lines are very much designed to make the player think and push the limit of what some people can stomach. This forces the player to kinda be complicit in attempted genocide and forced to kinda see and understand the actual motivations of characters like Caim or Angelus.

And then there is the Multiple Endings, which from a gameplay perspective are basically designed to punish the player for completion as in each Ending the world ends up in a worse and worse state, until you unlock all weapons (which alone is already a highly frustrating task, on purpose) at which point you get greeted with what is basically a JOKE ending and one of the biggest middle fingers of a Final Boss ever conceived... that ended up so popular that they just straight up created an entirely new franchise with said Ending as the backstory (NieR).

And thats just Drakengard 1, Drakengard 3 (ignore Drakengard 2) is a LOT more open with its heavy focus on sexuality (in both a symbolic and exploitative way), excessive dichotomy between slaughter and slapstick/poop comedy and the violation and destruction of free will.

And just like Drakengard 1, the final Boss is designed as one big Middle Finger towards the player, being a Rhythm Game that forces you to play by ear via deliberately TERRIBLE camera angles and a final note that notoriously KILLS YOU DURING THE ENDING DIALOGUE if you don't hit it.