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Nightmare Fuel: Xenogears
Though a Teen rated game, it seemed to warrant a Mature ratingnote It actually did get the Japanese equivalent, a D rating; it gave plenty of warning to people who caught the reference to the movie Soylent Green (which would likely be lost on the T rating demographic), nevertheless, one scene in particular occurred in a green factory with a conveyor belt that had dead mutated people dropped on it that then went through giant grinders resembling sink garbage disposals.
The first scene where we see the mysterious red mech in action , which will later be revealed as being as Weltall-Id, to say that the sheer power and Hopeless Boss Fight at said time is terrifying is an understatement. Specifically, the people mutating into the grotesque Wels and becoming parts for Deus. And it's no small number of people either; everyone who doesn't have Plot Armor (mostNPCs) mutate. It's also implied they don't get better in the game's ending, and are killed along with Deus.