Despite the tone of the game being pretty light hearted for the first half, I'd say X and Y are arguably the darkest simply because of AZ backstory and how Lysandre wants to revive his weapon, and in Y he tries to kill the player out of spite for stopping him. It was also the first game to increase the series' age ratings in the UK and Australia.
Out of the games on this list, it's definitely Sun and Moon though. Aside from some dark Pokedex descriptions, Lusamine keeps countless "babies" which are frozen Pokemon that she kidnapped and tried to preserve so they'd never die, then she tortured Cosmog to make it open up Ultra Wormholes all over the island, despite knowing that she may kill it, and after finding out what the Aether Foundation is truly like Faba tries to get a bunch of Aether employees to "silence" you and gets you into a 6 on 2 battle to make sure you don't win.
Guzma is also still traumatized by his childhood and was apparently beaten with golf clubs by his own father (though this one was partially cut from the non Japanese releases).
