Don't let the cute and quirky character designs and whimsical settings fool you; all of the games have several examples.
- There's a few unknown sound cues which play whenever the player uncovers something mysterious or scary. The sounds can range from what sound like distorted howls to scary rustling.
- Whenever there's no music playing followed by a cue, it normally means something ominous is about to happen. Oftentimes, it can keep players on edge.
- The chapter screen jingles for Last Specter and Diabolical Box are pretty unnerving, to say the least.
- There's the scene where Simon is lying dead on the floor, believed to be murdered. Pretty unexpected. Sure, he's just a robot, but that hasn't been revealed yet at this point so it looks like a real murder.
- Then there's the scene where both Layton and Luke are nearly crushed by a remote-controlled Ferris Wheel...
- Bruno as a whole; if you ignore the misunderstandings NP Cs have towards him, is a generally creepy old man who comes out at night to kidnap random citizens to do god-knows-what to them. His sprite in the "mysteries" tab doesn't cut it either, portraying him as a genuinely evil person.
- The Tower he also resides in is purposefully creepy; it lights up at night simultaneously and ends up giving Layton and Co the creeps... Just what in god's name is going on there?
- The Sequel as a whole takes a turn for the dark as a genuinely more "somber" game, taking cues with a more dreary Art Noveau visual style, especially in the latter-half of the game. The entirety of Folsense, Herzen Castle, and the Train station depict a dark and ominous world, compared to the first game and others.
- In a fairly lighthearted game about solving puzzles, we get 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 just a nightmare caused by hallucinogenic gas, and 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 a toxic gas leak from a nearby mine (which is, truth in television). Everything about the town is cursed, and the worst part, everything the player encounters is most likely an illusion. What was really going on there?
- Since the gas in the town creates hallucinations which are close to what the victim expects, this means that the town can look completely different for people who don't enter through the train station. What if someone imagines the city to be something out of H. P. Lovecraft or anything similar? Well, then they actually see the town as exactly that.
- The folsense train station can be quite unnerving; with creepy music, a dark atmosphere, and very unsettling visuals.
- 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 presented as red herring, it still comes out of nowhere and is never explained.
- The Herzen Castle itself can count towards this, mostly because of its 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 the game with a mentally unbalanced Clive's mobile fortress rising from the ground, who then starts his plan to devastate London. It's not made clear if the area was evacuated, and if it wasn't, he may have killed a large number of people, although it's not brought up in-game.
- 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 Dmitri 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.
- Clive himself. While other villains in the series are fairly normal for their motives and don't really want to do anything extremely evil, Clive is the complete opposite of this. For the first time in a fairly lighthearted series, you see a person who's willing to commit acts of national terrorism to achieve his goals. Even though he attempts to redeem himself, he can't undo the damage he did.
- Even though Clive gets arrested in the end it's Bill Hawks who ultimately gets away with everything, meaning that he's free to do whatever he wants and continue to silence the truth.
- Dmitri's flashback in which he discovers Claire's dead body. All you see is her arm, but it's still unsettling, especially when one remembers this is a game for children.
- Subject 3's backstory. He was a cute little bunny, abandoned and orphaned, before he was captured and sold to scientists and subjected to a number of torturous experiments.
- The Spectre, especially the very first cutscene where it attacks the hotel.
- If that doesn't put you off, the ancient "mural" artwork which depicts it is also quite disturbing, giving the entirety of it's origin as an evil force.
- The stare it gives the trio when it's done bashing it's head into another building, with a cut a terrified look on their faces when they think they're about to die...
- And the Black Raven. True, when you find out who he is, he stops being so terrifying and becomes almost endearing, but at first...
- The Masked Gentlemen's stories told 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!"