Don't let the cute and quirky character designs and whimsical settings fool you; all of the games have several examples.
* In ''VideoGame/ProfessorLaytonAndTheCuriousVillage'', there was the scene where Simon [[spoiler: was lying dead on the floor, believed to be murdered. Pretty unexpected.]] Sure, he was [[spoiler: just a robot]], but still...
** Then there's the scene where both Layton and Luke are nearly crushed by a remote-controlled Ferris Wheel...
* In ''VideoGame/ProfessorLaytonAndTheDiabolicalBox'', a fairly lighthearted game about solving puzzles, we get [[http://www.youtube.com/watch?v=ixTc8Z-TelI this]]. Just watch it until the end. It starts out as a dance scene, and then it turns into some sort of vampire movie scene. It turns out that this was [[spoiler: just a nightmare caused by hallucinogenic gas, and that Anton wasn't really going to eat them]], but still, it was pretty unexpected for an E10+ game, especially during such as light scene as that one.
* Folsense could count as this with the eerie atmosphere and the entire idea of the town itself. The town is essentially a boom town abandoned due to [[spoiler: a vein of deadly gas that drives half of the town's population away]]. Everything about the town is cursed, and the worst part, it was all probably all an illusion. What was really going on there?
* In one scene of the dark forest, Luke feels a ghost watching him, and is reassured by Layton that it was just his imagination. While it's most likely a small part of the story, it still comes out of nowhere and is never explained.
* The Herzen Castle itself can count towards this, mostly because of it's jarring appearance compared to the rest of Folsense and the seemingly bottomless pit with ruined mining facilities underneath. It's a surprise the castle even stands, to be honest.
* There's a blood stain next to an axe and a pair of manacles in the castle's equipment room. What happened there?
* The unforgettable climax of ''VideoGame/ProfessorLaytonAndTheUnwoundFuture'' with Clive's mobile fortress rising from the ground, who then starts his plan by ''destroying hundreds of houses and killing hundreds of people, ALL SHOWN ON-SCREEN.''
** The flashbacks to the time machine accident ten years ago are also pretty bad - which one hits hardest will depend a lot on you, but Dimitri finding Claire's body after arriving minutes too late to stop the experiment, Layton's description of the powerful hushing up the deaths of ten people, and young Clive's utter breakdown at realizing his parents are dead are all candidates.
** Hell, the entire attack on London is enough to trigger a nationwide catastrophe. Nations around the world would be put on high alert, military forces would have been mobilized by the time the Fortress attacked, and weapons systems would have probably been arming for a strike. It's not so far from the truth to say that a massive world war could have happened if Clive wasn't stopped in time. And even then, it doesn't stop other nations from using similar weapons to unleash destruction on a similar scale.
* The player can come across military weapons such as tanks and missiles in the laboratory. What was Clive planning to do after he destroyed the city?
* And in ''VideoGame/ProfessorLaytonAndTheLastSpecter'', we have, well, the Specter.
** And the Black Raven. True, when you find out who he ''is'', he stops being so terrifying and becomes almost endearing, but at first...
* Then in ''VideoGame/ProfessorLaytonAndTheMiracleMask'', we get The Masked Gentlemen's stories near the end of the game. To elaborate, The Masked Gentleman giving out clues to his whereabouts. The first story is a pleasant, if slightly somber tale about connections to your past. But then the second story talks about how greed takes over someone's life, causing everyone to leave, ending with the tale stating that he was a lonely king in a lonely kingdom. THE END. If that wasn't enough however, it gets more horrifying in the third tale. This one depicts a princess falling in love with a knight, and they are then married. The knight leaves to fight a dragon and never returns. Stricken with grief, the princess then turns to the chancellor and the two get married. It is then explained that said chancellor collapsed the cave where the knight went to fight the dragon. He now has the princess and the kingdom and ends with "ALL'S WELL THAT ENDS WELL!"
* There's quite a lot in ''VideoGame/ProfessorLaytonAndTheAzranLegacy''. For starters, in Hoogland, they're doing [[spoiler: A HUMAN SACRIFICE RITUAL TO THE 'DRAGONLORD'!]] And also, Aurora remembers something so terrible that [[spoiler: she almost commited suicide.]] And let's not forget that [[spoiler: Bronev pierced Aurora's heart with ice. Even if she was a golem, Bronev didn't know that. If Aurora was a human, she probably would have died.]]
* The concept for the new Lady Layton game is scary if you think about it. Here you are playing as the new protagonist, Layton's daughter, and it's mentioned in the trailer that her father has gone missing. Yeah. Professor Layton, the puzzle solving, fence wielding, death defying, kick butt and take names gentleman whom we have grown to love... is now MISSING! Just how evil is the new villain of this story?!?
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