This is my summary of the game as I go.  It will feature SPOILERS but no puzzles or solutions.  It's mostly for people who don't have the game but want to be spoiled on the story.  It'll be updated as I play.

Last updated 12/10/12
Prologue

The game opens with a car chase.  A man in a suit and cap is behind the wheel, Mahoney with him, as they swerve down an empty street at night.  He gives her a slip of paper and tells her that if anything happens to him, "he" will help her.  They're attacked by a flock of one-eyed flying-things that the cap-man refers to as "witches."  Using some kind of magic, the witches bring to life a pair of stone statues that send the car flying off the road and into a tree.

Mahoney wakes up next to her friend, but he's been injured, and he tells her to leave without him.
  She snatches up what looks like a book of magic and runs into the fog just as a bunch of cop cars pull up, Inspector Chelmey at the head.


Meanwhile, Layton and Luke are in London discussing the existence of witches and witch trials.  Layton dismisses the existence of magic.  We then see Phoenix and Maya aboard an airplane, where we learn that Phoenix is headed to a law conference in England, and doesn't expect or intend to stand in court.  Maya teases him that anything is possible, and as Phoenix scolds her for being foreboding, a witch-thing streaks through the clouds and we get a title screen.

Chapter 1

Back to Layton and Luke in Layton's office.  As they chat about the weather and teach me how to investigate, I find my first puzzle (ironically enough, involving witches).  As Layton and Luke plan to retire for the night, there's a knock on the door.  It's Mahoney, and she gives Layton the letter her cap-friend gave her.  Layton does us the favor of giving us the gentleman's name: Jovanni, one of Layton's old students now working as a detective.  Layton opens the letter and begins to read.

"Professor Layton.  It's been a long time.  There's much I'd like to tell you, but I have no time.  My life is in danger from a terrifying force.  I don't know if I can escape.  It all began in a strange town, known as "Labyrinth City."  You won't find it on any map.  I stumbled upon it during an investigation, and ever since then, all manner of mysterious and unbelievable things have happened to me, one after the other.  I just knew there was a secret to this place, and I sought to uncover it.  ...But they caught on to me.  I escape there with a young girl named Mahoney.  I believe she is the key to the city's mysteries.  They're after her, not me.  So please, protect her for me.  That city holds a great secret.  Too great for me, as it seems.  Forgive me for laying this burden on you. 

Your student, Jovanni Jicore."

Mahoney explains that Jovanni was injured and begs for Layton's help, but Layton is confident that Jovanni's all right, and that he's more concerned about Mahoney.  When he asks exactly what is after her, he and Luke are shocked to hear she's being chased by "witches."  She insists that there's no escaping "the eye" and that she probably shouldn't have come, but protecting fine young ladies is just what a gentleman does, so that settles that.

As they figure out what to do next, they discover that Mahoney has never heard of London or England and doesn't know how she got there.  She hands over his book, the Labyrinthia, which glows when Layton opens it.  Mahoney claims that all of Labyrinth City's "stories" are written in it, from past to future events.  As they ponder this, a pigeon flies to the window.  Luke lets it in, but the pigeon immediately turns into a witch and makes off with Mahoney.  Layton and Luke resolve to save Mahoney and hurry off.

In the shadow of the Tower Bridge they run into Chelmey and Barton.  Chelmey admits that a strange accident has occurred, and he directs Layton to the wreck of Jovanni's car in a tree.  After convincing the officer on duty via puzzle that he has permission, Layton investigates the car and notices a huge handprint on the hood of the suspended car.  Chelmey confirms that the driver, Jovanni, survived the crash with minimal injuries, and Barton lets slip that he saw someone in a "Halloween costume" heading in the direction of the bridge.  Naturally, Layton and Luke pursue. 

At the bridge they see and follow a figure in a black cloak, but it vanishes inside a tunnel.  They notice Mahoney's cloak nearby a wall, and when they investigate, a symbol set into the wall triggers a secret door to open.  Inside is another tunnel, with Mahoney tied up at the mouth.  They release her, but before they can make a run for it strange noises come from inside the tunnel as the witches come for them.  Layton convinces Mahoney to leave everything to him.  While Mahoney manages to escape on a passing boat, Layton draws the witches away with the help of Luke in a Mahoney-disguise (complete with magic book).

The head witch is not happy about falling for the fake out, but then she taunts Layton and Luke, telling them they don't know the danger they've put themselves in by "stepping into the story."  She then disappears.  As Layton and Luke ponder her words, the magic book begins to rattle, and when it opens, our heroes are shocked to see themselves drawn into the illustrations.  The drawings swell from the pages and we fade to black.
Chapter 2

The scene changes to a security guard as he comes across a violent struggle between two women in a storage room.  One strikes the other down with a steel pipe: the attacker is Mahoney! 

In the courtroom lobby, Maya teases Phoenix about getting put on a case after all.  Maya pulls out a newspaper announcing the appearance of a group of jewel thieves in London (Chelmey is pictured in the article).  But Phoenix says that can't be the case they're on, they're not IN London, and they're supposed to be participating in a practice case only, not a famous jewel theft.

The door opens, and in steps Jodorra, introducing herself as a professor of law at Stella Private Academy.
  Her student, Mahoney, is with her (Mahoney is dressed as a student but her eyes are disturbingly vacant).  Jodorra assures Phoenix that Mahoney's already confessed, so the trial should be simple.  She starts to hand over the necessary evidence and information but is called away before Phoenix can see it.  As soon as she's gone, Mahoney says, in creepy monotone, "I am not a witch."  Phoenix is then called into court.

The judge introduces the accused as Mahoney Katalucia.  The prosecutor is Bartely who, in true Payne fashion, taunts Phoenix obnoxiously.  Phoenix finally has the chance to look at the court record and learns that Mahoney has been charged with theft and assault.  The victim was struck in the back of the head with a rod-shaped item that left lacerations, but has since recovered.

Bartely outlines the case.  The case took place on board a ship moored on the River Thames.  It was preparing to depart with its cargo when the accused snuck aboard.  A security guard caught her red-handed in the act of smashing one of the crew members over the head with a pipe.  The cargo she was trying to steal was a stuffed animal of none other than the Blue Badger, which the London police have adopted as their mascot.

The security guard is called to the stand.  It is immediately apparent that he takes his job very seriously.  He strikes a pose and introduces himself as Yutorino Gardner.  He testifies to seeing the assault and catching Mahoney, but when he insists that nothing else in the cargo hold was disturbed, Phoenix indicates an open crate in the crime scene photo.  Yutorino's pride as a professional is wounded, and he insists it's not his fault that he missed it, because the electricity was out and he only had the emergency light and his trusty flashlight to see with.  The flashlight is entered into evidence, Yutorino's fingerprints clearly visible on it in smudges of chocolate (his favorite).  But Yutorino's testimony is called into question again when he admits he was wearing his sunglasses at the time, and is under the false impression that Mahoney hit her victim from right in front of her rather than from behind, as the victim's wounds indicate.

Phoenix declares that his client is innocent, and the Judge agrees that further inquiry is needed.  Bartely lets slip "This isn't what I was promised!"  But Yutorino isn't finished yet.  He claims Mahoney can't be declared innocent since she's also accused of theft, and he has proof that she's definitely guilty of that.  He has a gold tag with "London" written on it that is supposed to be wrapped around the Blue Badger doll, which he discovered in the victim's hand.  He supposes that the victim tore it off during the struggle, which means Mahoney must have been trying to take the doll with her.

Bartely tells Phoenix to just give up, since Mahoney's already confessed anyway, but Phoenix insists they continue.  Court goes into recess while the next witness is prepared.

In the defense lobby, Phoenix and Maya congratulate themselves on earning their client a fighting chance.  Jodorra, however, seems less than pleased.  Maya spots her reading the newspaper they discarded earlier.  When she notices them, Jodorra quickly discards the paper.  She scolds Phoenix for getting carried away and insists that Mahoney has already confessed, and that pushing for acquittal will only harm her delicate sensibilities (and cause the Academy undue embarrassment).  She urges him not to make a fuss over just a "stuffed animal" and then leaves.

The witness is called, a young woman in a chef uniform named Olive Aldente.  She just happens to be carrying her cleaver with her.  Bartely confirms that she was the victim in this case that was struck by Mahoney.  She testifies that she went to the cargo hold to check up on her cooking ingredients.  When she saw Mahoney trying to sneak off with the stuffed animal, she intervened, and was struck with the pipe.  Bartely introduces a new piece of evidence: a picture of the fingerprints clearly visible on the pipe.  There were no other prints on it.

Even in the face of such damning evidence, Phoenix is determined to continue.  He points out that the position of the fingerprints on the pipe are backwards, making it impossible for Mahoney to have swung the pipe like a bat.  Olive claims that Mahoney did hold the pipe backwards, and struck her in a backhand, but Phoenix says again that this isn't possible.  Given that Olive is taller than Mahoney, it's impossible for Mahoney to have struck Olive in the back of the head using a backhanded swing.  In fact, the prints only make sense if Mahoney was trying to grab the pipe as it was swung at her head.  Mahoney wasn't the attacker, she was the victim.  Phoenix accuses Olive of being the attacker, pointing out that her gloves would have prevented her from leaving prints. 

Olive denies it.  She wildly accuses the security guard, since he was wearing gloves, too.  But Phoenix presents Yutorino's chocolate-stained flashlight as proof that he wasn't wearing gloves that night. 

Bartely protests the defense's baseless speculation.  He insists that Mahoney has already confessed, and he presents the stuffed animal in question as proof.  The Blue Badger (wearing a London police cap) is missing a leg that was torn off in the struggle.  As Bartely shows it off, Phoenix notices that Olive flinches.

Olive testifies that she was the one to return the doll to the police, as she was able to pull it away from Mahoney during their struggle.  She claims that she couldn't have been the one to swing the pipe around because she was clinging to the doll with one hand the entire time.  Phoenix presses her to confirm that this exact doll is the one, and when Olive says it is, he points out that this doll still has its gold London tag.  Yutorino already testified that he discovered Mahoney holding the tag she took from the doll she stole, so why does this doll still has his?

Olive says that maybe Yutorino brought a fake tag on his own just to cause trouble, but Phoenix says all they need to do is check the tag for prints.  In the meantime, why not search the ship for a doll that's missing a tag?  Olive must have swapped dolls for some reason.  Bartely doesn't understand why anyone would do that, considering all the dolls are the same.  Phoenix argues that's exactly the point.  Why would she change the dolls?  All they need to is search the ship to know for sure.

Olive freaks out and begs them not to.  The judge asks Phoenix to present one final piece of evidence to prove why a search is even necessary, so he presents the newspaper Maya had earlier.  The ship they're talking about just came from London, where priceless jewels have just gone missing.  Phoenix speculates that the missing jewels were hidden in the doll, which is why Olive was desperate to keep it hidden from the police.  Olive has a breakdown.

The search team reports from the ship, having discovered the doll with the missing tag and a 100,000 pound pink diamond inside.  They also found Mahoney's prints on the tag provided by Yutorino, confirming Phoenix's version of the events.  Olive admits that she's part of the group that stole the diamond.  They had been doing it for a while, one jewel per doll.  When she went to the hold to retrieve it and found Mahoney there, she assumed that Mahoney was trying to steal it and did everything in her power to keep the diamond safe.  She also doesn't know who it was that struck her in the back of the head.  At first she thought it was Mahoney, but now she thinks it may have been a witch.

The judge thanks Phoenix for his service to the court and tells Bartely that he could learn a thing or two.  He then declares Mahoney innocent.

Back in the defense lobby, Jodorra sure doesn't look happy, but she thanks Phoenix and encourages Mahoney to do the same.  Mahoney does so, clutching a heavy book (the Labyrinthia) to her chest.  Jodorra compliments Phoenix again on his skill and departs with Mahoney.  While Phoenix and Maya wonder about where Olive's attacker disappeared to, they notice that Mahoney left her book behind.  Maya opens it up and finds a illustration that includes the two of them inside.  The book starts to glow, and Phoenix and Maya disappear into the book.
Chapter 3

Latyon and Luke awake in the back of a horse-drawn carriage, accompanied by a woman in a cloak (who looks like Jodorra).  They ask where the carriage is taking them, but she brushes them off, saying there's no reason to ask when there's only one place to go.  They try asking the old woman driving the carriage, but she makes fun of them and finally suggests they just look outside, since they've arrived.  Layton and Luke peer through the curtains and find themselves in the medieval Labyrinth City.

 

Nearby, a group of knights gather.  Their captain is approached by two children, Gure and Teru, who want to be knights, too.  Melune the bard serenades the lovely Lady Pupurin.  Layton and Luke take in the strange city-dwellers in astonishment and realize they're in the same scenery depicted in Mahoney's book.  As they speculate on how they got there, Jodorra speaks up, telling them that it was "decided."  As far as they should be considered, the London they came from--or anywhere else outside the city--doesn't exist.  In fact, the road they took coming into the city doesn't even exist anymore, and the gate has been replaced with a solid wall.

 

Jodorra disappears.  Layton and Luke resolve to ask the surrounding cityfolk about their circumstances, and attract the attention of the knight captain.  The knight doesn't know anything about the disappearing gate, and in order to appease him, Layton plays along by saying that they're actually just lost residents.  By now the captain is suspicious, so he tests Layton with a puzzle.  Some things stay the same in both worlds, apparently!

 

Impressed by Layton's puzzle-solving abilities, the captain lets them go with a warning to be on their best behavior, as today is a very special day.  As he leaves, Layton and Luke decide to try and pick up Jovanni's trail, assuming that since he was able to escape the city somehow, there must be a way.  As they move on, a shadowy voice talks to itself about how they will soon learn what their role in this story truly is.

 

Layton and Luke are then approached by Gure and Teru, who are none too pleased with two strangers waltzing into "their turf."  Luke wins them over with a puzzle, and is accepted into their gang as a lackey.  They're now able to move around the town.

 

At the center square, they meet Melune the bard, who gives them a map (via puzzle) which gives them access to even more of the city. They also meet Pupurin, who is swooning over the captain of the guard.  In the shopping district, they met Peter, and ask him about Jovanni.  Peter says hasn't heard of anyone by that name, and suggests they just concentrate on getting ready for the big event coming up.  Of course, he won't just tell them what that is. 

 

Some puzzles later Layton and Luke are drawn to the north of the square where "he" is arriving.  Just about everyone in the city seems to be there for it.  A woman named Bertha tells them the city's creator, The Storyteller, is about to arrive.  A huge entourage approaches, including a parade of knights and a float bearing a gray-haired man with half a mask (The Storyteller).  The crowd showers him with praise.  Jodorra is with him, and she and the knights shower the people with paper, declaring it "a new story."  She and Layton share a lingering, unfriendly stare.

 

The procession moves on, and in its wake, the cityfolk change their tune.  As they read the scattered papers many get scared and leave.  Luke grabs one up and reads aloud.

 

In the depths of the moonlit forest,

A terrifying witch casts a shadow of death.

Once two anxious young people step foot into the darkness,

Their lives are bewitched, burned, and finally put out by "The Demon's Fire.

 

Luke tries to calm the cityfolk by reassuring them that it's just a story, which sends them into fits of disbelief.  The commotion attracts the captain from earlier, who is shocked to hear that Luke doesn't believe in the Storyteller's stories.  The crowd swiftly turns against them as they connect the two strangers to the two "young people" in the Storyteller's story meant to die.  Just as the knights move to arrest them, they hear a voice calling them from a nearby side street, and they make a run for it.  They find Mahoney in a dark alley and hide until the guards have passed.  Mahoney then leads them to safety.

 

Layton asks Mahoney how she got back to the city after they left her on the boat, but she doesn't quite remember.  Layton and Luke can't explain how they got there, either.  Deciding that they need to find a secure place to sit and talk, Mahoney suggests they go to Mrs. Kurowa, the breadmaker.

 

They arrive at the bread shop, but instead of finding Mrs. Kurowa, they meet Phoenix and Maya!  For some reason, they're happily (and vigorously) making bread, and they greet Mahoney very cheerfully.  Introductions are passed all around, with Maya declaring Phoenix her "top apprentice."  Maya explains that she and Phoenix have been working at the shop for the past five years, and are good friends of Mahoney.  She decides to make Luke special bread on the house.  Phoenix tries to serve them some with a TAKE THAT, which Maya quickly scolds him for.  Guests are not for defeating, Phoenix!

 

Mrs. Kurowa returns, and at first is quite the pleasant lady, but things turn ugly when Phoenix and Maya make a few disparaging comments about bread!  Mahoney retreats with Layton and Luke to her room while Phoenix and Maya endure the wrath of The Boss.

 

In Mahoney's room, they meet her cat, Croney.  At first Mahoney has some trouble remembering everything that's happened so far, but a glance at Jovanni's letter reminds her.  She admits that Jovanni was in Labyrinth City with her--in this very shop, but she doesn't remember going to London or anything that happened there other than meeting Layton and Luke.  As far as she knows, she's just been working with Phoenix and Maya in the bread shop, but she admits she doesn't really trust her memory.

 

Layton continues to press her, and she suddenly remembers Jovanni saying something about the stories collected in the Labyrinthia shining light on the city's mysteries.  To her (and everyone else in the city) the Storyteller's stories becoming truth is obvious and understood, and she doesn't understand how Layton, and Jovanni before him, can doubt that.  She recalls that Jovanni often went to the Grand Library, where all the stories are kept.    There are even stories about witches there.  Because it's the job of the knights to find and capture witches, they take those stories very seriously. 

 

Mahoney lays it out for them.  First there's The Storyteller, the city's creator responsible for creating all the stories, including the current witch incident.  Next are the knights, charged with protecting the people from those incidents.  They also serve as The Storyteller's bodyguards.  Lastly, there are the inquisitors, the ones who prosecute witches captured by the knights.  The three of them form Labyrinth City's ruling government.  They all come out together to spread the most important stories, like that morning.  They all decide to head to the Grand Library, but not before Mahoney's cat brings her her favorite pendant to take with her.

The three of them head to the Grand Library, and enormous building at the north end of town.  Luke notices a portion of the roof seems to have been burned in a fire, and while Mahoney hesitates to explain, they're approached by Peter.  He's shocked that they don't know the story behind the Legendary Fire, which happened some time ago.  Taking pity on their ignorance, he explains that many years ago a huge fire engulfed most of the city, and the scorch marks on the library are from that.  As Peter leaves, Mahoney looks troubled, but she brushes aside Layton's concern and they continue inside.

They meet a young librarian, Buck, carrying a large stack of books.  When he notices Mahoney he panics and almost drops them, and then again when he learns that Layton and Luke are interested in finding books about magic.  He tells them that if they want to borrow the Encyclopedia of Magic, they'll have to ask the head librarian, Nazomy Steria.  Nazomy appears as if on command, and is appalled by the request.  She scolds Mahoney, telling her that she knows very well what that book is and that it would be impossible for her to hand it to anyone.  Layton tries to smooth things over with a gentlemanly introduction, and learns that he'll need permission from the Inquisitors to even get a glimpse of the book.  But because this is a Layton game, Nazomy agrees to test Layton with a puzzle instead.  It takes more than one, but Nazomy finally admits defeat and agrees to lead Layton & Co. to the second floor reading room, where the book is kept.

They begin paging through the book, and come across two pages with letters written at a strange diagonal.  It reads:

Time has led you here.
The ancient flame,

sealed within a cage of endless books,
waits for the time to awaken.
If the sun and moon that watch over the wise scholar cross paths,
taking on their true form,
the flow of time will reverse,
allowing the "door" to open.
But in the end, he who challenges the great mystery
will end without having completed his role.
The door remains unopened.
I will wait for the time to awaken.

 

Nazomy claims she's never seen the writing, and doesn't know how it got there, seeing as she has the only key.  They speculate on whether or not a witch is responsible, but Layton changes course, suggesting that the text refers to Jovanni, and the "cage of books" is the library.  He resolves to search the library for the "mystery" referred to, and the "door."  Nazomy gives them permission to investigate and they gather at the library entrance.

 

Layton proposes that all the clues point to the library itself.  They spot a relief featuring a sun and moon overlooking Nazomy's desk (making her the "scholar" in the riddle).  A puzzle later and a secret door opens in the floor.