9. All Your Friends Try To Kill You - Pokémon Mystery Dungeon: Rescue Team Red/Blue
With the exceptions of perhaps Gale of Darkness and Pokémon Coliseum, Pokémon as a franchise has always been entirely crafted for kids. This isn't to suggest that it doesn't occasionally explore dark or complex themes, or that enjoying training and evolving your team is somehow childish - it's just been consistently clear that creators have been careful to make sure young and old audiences could both enjoy the series.
However, the plots of some games do, at points, notably veer into more messed up territory than you might expect a child-friendly franchise to delve into. Though we all remember that ghost girl in X and Y, or the suggestion that Guzma was abused, there's actually a weirder moment in the main plot of Pokémon Mystery Dungeon.
After tirelessly working to try and help the townspeople and surrounding 'mon with their issues, they will immediately turn on you when the (very clearly evil) Gengar suggests that you are the reason for the calamities currently befalling the world.
It's not played down, either. They explicitly want to kill you, all because some guy has suggested bad things are your fault. All the good deeds before? Apparently they don't matter now, because it's time to get slaughtered by your former friends.