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Layton and Luke search through the eponymous St. Mystere for the Golden Apple, which was hidden there by the late Baron Reinhold; the will of the baron states that whoever finds it will inherit his immense wealth. Of course, the village hides quite a few secrets as well...
Please place series-spanning tropes on the main Professor Layton page.
- Abhorrent Admirer: Martha, an old woman with a lisp Layton and Luke meet on the way to the tower.
- Absurdly Spacious Sewer: Sylvain and Stachen both go down there to relax, apparently.
- Artificial Human: Every single character, except for the recurring cast, Bruno, and Baron Reinhold. Matthew, at least, was a real person at some point.
- Batman Gambit: Baron Reinhold created the whole village so that only somebody clever and caring enough would discover his fortune and use it to care for his daughter. Unfortunately, there's the chance that a clever man would get to Flora, then a caring one would be led to the treasure. This in turn creates the chance that Flora would be stuck with a greedy - but smart - Jerkass, and no money. He might have been assuming that a Jerkass would just ditch her when he found out there was apparently no money and she could go back to waiting for the right person, but that leaves the question of what they'd do with a person like that to keep the village's secret from getting out.
- Bruno was there to watch people entering the village, to make sure they were morally worthy of finding and caring for Flora. Additionally, an evil clever person probably wouldn't have made Flora happy, and therefore never found her "birthmark" or the location of the fortune.
- Big Eater: Prosciutto, who has Jabba Table Manners to boot.
- Bizarrchitecture: How in the world does that tower stay upright?!
- Captain Obvious: If you tap on the stairs in the inn, Layton says, "These stairs lead to the second floor." You know, like stairs do.
- Cats Are Mean: When Luke tries to pick up Lady Dahlia's cat, it scratches him clear across the face and runs away...which requires them to go chase after it.
- Closed Circle: St. Mystere, starting shortly after the game begins.
- Due to the Dead: Baron Reinhold had an elaborate tomb built in the garden for his first wife, Flora's mother, so that she would always be close by. It's unclear how long he lived after her death, but the pages of Bruno's journal seem to indicate that his excessive mourning contributed to his own early passing.
- Easter Egg: In the "Painting Scraps" tutorial, if you look closely at the sample painting that is in the process of being pieced together, you can see that it is the picture of Professor Layton and Luke from the cover of the game.
- Ferris Wheel of Doom: Almost runs over Layton and Luke.
- Foreshadowing: When Layton and Luke meet Flora on the top of the tower, they learn that her father told her that the person who solved the mystery and came to get her would be someone she could trust with her life. A few minutes later, when Layton, Luke, and Flora are fleeing from the crumbling tower, the stairs collapse and Flora nearly falls to her death... but is pulled back in the nick of time by Layton, thus proving her father's words correct.
- And prior to this, while Layton and Luke are climbing the tower, they have to solve a Klotski puzzle called "The Princess in the Box." The puzzle's description urges the player to help the princess escape from where she's being held.
- Fortune Teller: One of the villagers, Agnes, insists on reading Layton or Luke's fortune in exchange for their solving a puzzle. She invariably predicts bad luck.
- Getting Crap Past the Radar: At one point you are required to look for a clue in the painting of a girl. Touching the general area of the breasts will result in a comment from Layton. Because of the proximity to the place where you are meant to touch (which is made obvious), it's entirely possible to find this accidentally.
Now, Luke, it's important to be a gentleman.
- Gilded Cage: St. Mystere is essentially this to Flora, who can't leave until a worthy guardian solves the mystery of the Golden Apple.
- Girl in the Tower
- The Greatest Story Never Told: "No, Luke. St. Mystere's secret must stay between us. We don't want to make a spectacle of Flora."
- Heir of Mystery: The main plot. Layton and Luke have to find the Golden Apple in order to inherit the late Baron Reinhold's wealth.
- Hurricane of Puns: Giuseppe, the butcher, can't resist cramming meat puns into everything he says, and if he can't make it work, he'll force it anyway.
- Impersonating An Inspector: Don Paolo impersonates Inspector Chelmey.
- Insistent Terminology: Characters constantly refer to Layton as a detective; he gets just a bit annoyed at this, since he's actually a university professor of archaeology.
- Interface Spoiler: If you look up the details on the "Vanishing Crank" mystery as soon as it's listed as "Solved," it will give away the fact that the true purpose of the will was to find a suitable guardian for Flora shortly before it's revealed in the plot.
- An Interior Designer Is You: Perfectly furnishing Luke and Layton's rooms at St. Mystere's inn unlocks bonus puzzles.
- And Your Reward Is Interior Decorating: You acquire the furnishings by solving puzzles and progressing through the game.
- I Should Write a Book About This: Percy, a villager found near the clock tower, is an aspiring novelist who decides to write a mystery story based on Professor Layton.
- Luck-Based Mission: One Poor Pooch has at least 3 variants of the "correct" solution. Figuring out which one the game wants (the legs form an "x" shape, rather that two > or <) is pure luck.
- Meaningful Name: St. Mystere, French for Saint Mystery.
- No Hugging, No Kissing: Averted by Flora, who wakes up after the escape from the tower, laughs, and throws her arms around a surprised (but amused) Layton. And it is adorable.
- Obstructive Bureaucrat: A benign one of these can be found in the town hall, pestering Layton about paperwork and telling him it would be wise to leave town once he finishes his business.
- Old Retainer: Bruno's journal pages seem to imply that he sees himself in this light.
- Replacement Goldfish: Lady Dahlia was originally built as a replacement for Violet Reinhold. However, when Flora was terrified by the robot copy of her mother, the Baron realized this was impossible and had the robot's memory wiped and the Lady Dahlia personality created instead.
- Ridiculously-Human Robots: They can even vaguely remember deleted memories and dream when they sleep!
- Robo-Family: A few different kinds of robo-family relationships are present in this game. There's the aforementioned Dahlia, who is a robot spouse to the baron, as well as Simon who was built into the Reinhold family. Then there are a few families in the village.
- Robot Dog: What you get once you've picked up all of the "strange gizmos" in the village. It sniffs out hidden puzzles and hint coins.
- Soft Glass: After Layton reveals that "Chelmey" is really Don Paolo, he exits Reinhold Manor by smashing through a closed window.
- Solve the Soup Cans: Justified, as much as this kind of plot can be justified, by the ending: the many puzzles are to ensure anybody without an above-average intelligence wouldn't ever reach the top of the tower.
- Title Drop: At the very end:
Flora: The people who live here have been with me for so long. Curious as this village is, it's watched me grow up.
- Uncanny Valley: In-universe example with Lady Dahlia's original persona.
- Welcome to Corneria: Justified by the fact that, in retrospect, it's more surprising that the Baron's handyman could make robots capable of holding conversations at all.
- Your Tomcat Is Pregnant: According to the profiles, Claudia the cat is a he.
- Zillion-Dollar Bill: The Reinhold inheritance. It's heavily implied that touching it will kill (well, deactivate) all the robots, though.