Not quite as low profile as some of the other games being posted, but I'm not sure that any of the Professor Layton games had an ending twist/reveal that seemed even remotely plausible at the beginning of the story.
It say a lot when the game with everyone you talk to turning out to be steampunk robots is the most realistic and grounded. The worst one, for me, was the one where it turned out instead of ghosts the destruction of the town was because every night a sea monster and a giant robot had a kaiju fight (I think over a lost treasure). I did enjoy that in the time travel game they came up with a twist that was even less believable than time travel too.