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Prologue: So We Meet AgainEdit

The game begins with Professor Layton in his office at Gressenheller University. His housekeeper, Rosa is given a letter and she enters the room and catches Layton sleeping on the couch. She begins nagging at him and hands Layton the letter. After reading, he finds that the letter was from an old friend by the name of Clark Triton. Layton then rushes out of his office to his car. On the way out of London, Emmy Altava sees the professor's car and immediately chases him down. The two finally meet and Layton and Emmy finally put aside their differences, and she joins him as his assistant, aiding with the mystery of Misthallery.

Chapter One: The Fog of MisthalleryEdit

Once Layton and Emmy arrive at Misthallery, they begin searching for Clark's house. Once they have located the mayor's residence, Clark is delighted that Layton stopped by for a visit, but when Layton asks about the letter, Clark doesn't know what he is talking about. Clark then explains that his son, Luke, has been holed up in his room and avoiding Clark as of late, so Layton decides to talk with him.

Chapter Two: The Boy Who Foretold DisasterEdit

Layton and Emmy discover that Clark wasn't the one who had sent the letter, but Luke. Luke explains that the reason that he had sent the letter was because he predicted the world would end soon, because of a specter destroying the town. At first, Layton was doubtful about there being a 'specter' in the town, though Luke insists, so Layton and Emmy continue to look.

Chapter Three: The Specter AppearsEdit

While beginning their investigation of Misthallery, Layton and Emmy bring Luke to help their search for the specter and to help crack the case. Luke acts as a tour guide, showing Layton and Emmy around the town. As the group looks around, they find many eccentric characters and inhabitants of Misthallery. The trio rent a hotel room. After a small day's work of investigation, the three spend the night at the hotel, which lies on the street of where Luke predicts the specter will attack next.

After dark and within the hotel, the three hear strange echoing music and suddenly, they find themselves face-to-face with the specter. Layton instructs Emmy and Luke to rush to the window to get a better look at the specter. As Emmy takes a picture of the monster, it attacks the near-by hat shop and tears its claws into the very hotel that the trio is in. Layton begins to run out the door to chase down the specter, only to be stopped by a worried Luke. After a small talk, the trio move off into the now-soggy street that lies before them.

Chapter Four: The Shadowy Manipulator Edit

As dawn arises, Layton, Emmy, and Luke proceed with their investigation, searching areas on the western side of Misthallery. After some careful thought, Layton solves the riddles of the many kids that were running about the marketplace. Following their search throughout the market, more and more stories and thoughts on the nature of the specter begin to arise. Suddenly, as the trio were walking about the central plaza in the market, a shadowy, cloaked figure jumped from a chimney atop one of the buildings.

This figure, called the Black Raven, jumps down and dodges a kick by Emmy. A great chase ensues as Layton and Luke begin chasing down the Raven on foot. Emmy, however, follows the Raven onto the rooftops, showing the inhuman speed and agility the Raven possesses. The Raven then confronts Layton in the plaza and the two begin speaking about the black market, a place where Luke said the Specter's Flute was sold. After the talk, the Raven gives them access to the black market, and Layton enters the dark tunnel below the marketplace.

Within the black market, the trio find Crow, leader of the Black Ravens. Crow tells the professor and his assistants that he indeed sold the flute to highest bidder on day. That highest bidder being a Mr. Evan Barde, a wealthy man at the high end of town that died the year before. With this new information, Layton begins to set his sights on Barde Manor atop Highyard Hill.

Chapter Five: The Witch's Castle Edit

Luke takes Layton and Emmy to the arch that separates Misthallery from Highyard Hill, the location of the excavation sight for the legendary Golden Garden as well as the location of the police station. However, Layton is more focused on Barde Manor and thus, wastes no time on getting there. The three arrive at the eerie manor only to find that the gardener, Seamus has locked the place up tight. Layton and Emmy find it odd that there is a gardener for the manor, yet the garden of the place is badly unattended. Thus, more suspicion spreads and Layton, Luke, and Emmy try and find a way into Barde Manor.

Near by, there is a tower that leads into Barde Manor that Luke finds can help the three enter the manor. With their combined intellect, the three climb the tower and make their way into the manor. Inside, they meet Arianna Barde, the supposedly cursed "witch" of Misthallery. Luke tries to calm Arianna down, but unfortunately fails to do anything at the time. Seamus then enters and kicks the professor and his assistants out of the manor. Afterward, the three try to find information around Highyard Hill as the manor had been no help.

After some thought, Layton, Luke, and Emmy re-confront Arianna down by the lake shore by Barde Manor. At the shore, Layton tells the group in the area that Seamus isn't actually the gardener of the manor at all. He is actually Tony Barde, the younger brother of Arianna. After speaking with Arianna, Layton gathers more facts on the matter and begins to proceed back into Highyard Hill to investigate further matters. He then tasks Emmy to go back to London to aid the investigation from there by getting some files from Scotland Yard.

Chapter Six: London's Hidden Secrets Edit

Emmy takes her Emmycycle down into central London to Gressenheller University. Upon her arrival, she meets Dean Delmona, the dean of the university. After helping him with a riddle, she enters Layton's office and meets Rosa. While inside the office, she recovers a small book left by Layton to aid their investigation. She then heads off to Scotland Yard. While inside, she seeks out the help of Inspector Grosky, a high-class investigator of the yard.

Much to Emmy's dismay, he had recently left and thus, Emmy was tasked to track him down. After searching the museum and minor streets within London, Emmy returned to Scotland Yard. Upon her arrival, Grosky suddenly crashes through the window, wrestling with a criminal. With Emmy's help, the criminal is stopped and Grosky greets his old friend. With his help, Emmy then finds Inspector Chelmey and his assistant Barton. Inside the archives, Chelmey, Grosky, and Emmy find more secrets related to Mr. Barde's apparent suicide. With this information at hand, Emmy and Grosky race back to Misthallery.

Chapter Seven: Third Eye Jakes Edit

Once back in Misthallery, Layton, Luke, and Emmy meet Police Chief Levin Jakes. Upon the unsettling welcome of Jakes, Layton begins to question Jakes' role in Barde's death and what other mysteries which shroud Misthallery's recent past. With all this information regarding the new found mystery, Jakes begins to suspect Layton of murder and tells him to leave his office and then town. Jakes gives the professor 24 hours to leave Misthallery, or else.

After more searching across town, Layton and his crew are confronted by thugs and attacked. However, the thugs do not stand a chance against Emmy's fighting skills. This leads to the professor even more down a line of suspecting Jakes being a corrupt, vicious man. As night falls over Misthallery once again, Layton begins to think of a new plan of action against the specter. With the aid of the Black Ravens, Layton begins to create a small trap for the specter. With Luke's brilliant deductions, the three were able to predict the next position of the specter, and hopefully reveal what it actually is.

Shrouded in mist, Emmy, Luke, and Layton start to feel the quakes of the specter, and hear the tune of the mystic "Specter's Flute". Hiding in an alleyway, Professor Layton spots the eyes of the so-called specter and keeps to himself on what the looks of it actually are. Suddenly, however, dawn approaches and the three are captured by Jakes' men. The three are then taken to the police headquarters in Highyard Hill. Once inside, the three escape the interrogation room and leave. Once outisde, the group return to their investigation and head back to Barde Manor to discuss next steps.

Chapter Eight: Face to Face with the Specter Edit

Once the group returned to Barde Manor, the professor tells Arianna and Tony of what has been happening within the town, and Arianna then tells the group of a secret regarding what has been going on. She takes the Specter's Flute, an ocarina, in hand and walks down the pier. She plays the melody and suddenly, out of the lake before, a great monster rises out. Loosha, one of the last of her kind, rises and swims directly to Arianna and the professor. With Loosha uncovered, Jakes rises out of the shadows and fires net-launching guns at Loosha. Jakes' men then take Loosha hostage and flee to the central plaza in Highyard Hill as they suspect Loosha is indeed the specter that has been terrorizing the town.

Chapter Nine: The Specter Becomes ClearEdit

Layton, Luke, and Emmy then rush down into southern Misthallery to clear Loosha's name and save her life. Within southern Misthallery lies the old factory which had been abandoned for years. Fighting off a few thugs in the area, Layton and Emmy find themselves face-to-face with what has actually been seen as the infamous "specter". Luke then pilots this old mining device, one that was used in the hunt for the Golden Garden up north, and makes his way to the grand plaza in Highyard Hill.

Once at the plaza, Layton shows the people of Misthallery what has actually been the specter the entire time; one of the mining machines used for the Golden Garden. However, not only that, the professor then points out who was behind everything thus far. He points to Doland Noble, the Triton family's faithful butler. But, it would seem that he is not the real Doland at all. Layton shows the facts and tells him to reveal himself. Noble then puts on his hat and reveals himself to actually be the dreaded Jean Descole, a powerful man who uses his intelligence and scientific understanding to build powerful and deadly machinery.

Revealed, Descole activates dormant mining machines and takes a ride on the one Luke had brought to the plaza. Grosky leads most of the citizens to safety and Descole begins his assault on the town. The machines in the area fuse together become the 'Master Specter' and attacks Loosha. The two begin dodging each other's attacks, but Professor Layton gets caught in the crossfire, and Descole begins focusing his strikes more on him.

Chapter Ten: A Legend Revealed Edit

Solving plenty of difficult puzzles, Emmy breaks down Descole's machine, buying Layton enough time to build a catapult from scraps and pieces of wood. However, even after a direct hit, Descole's machine withstands the attack and fuses itself back together with ease. Loosha then runs up the hillsides and attempts to break open the dam. Descole, however, attempts to kill the professor wth the machine, but fails as the professor retakes to higher ground and gives Loosha and the Black Ravens enough time to begin their plan.

Loosha breaks down the dam's first set of flood gates and water begins to flood Misthallery. With the water, Descole's machine short-circuits and stops. After the machine stops, Descole tells the professor to savor this victory, as he has yet to win the war at hand. Descole then flees the area, leaving Loosha badly wounded. Layton, Arianna, Luke, Emmy, and Tony run to the dam with Loosha to uncover the final secret of Misthallery.

Epilogue: The Last Gift Edit

Loosha begins tearing down the dam's secondary flood gates, but Arianna tries to get her to stop, as it will flood the entire town. Layton and the rest take higher ground as the entire town becomes engulfed in water. Then the group follows Loosha into the lake and finds a strange sealed gate. Upon opening the gate, Loosha guides them through the tunnel into the Golden Garden, the sacred place Descole aimed to acquire. Once inside, however, Loosha collapses. Arianna and Tony comfort Loosha, but to no avail as Loosha dies and slides into the vast lake below. With the Golden Garden open, Luke and Arianna begin to think of the good that has come out of this. Luke tells Arianna that in her last words, Loosha said "thank you" to Arianna and Tony for the many years they spent together.

Arianna realizes all she has done wrong and with the help of Luke, Arianna regains her composure and plays the Melody of the Specter's Flute one last time in Loosha's memory. After playing the song, Layton and Emmy begin conversing over the discovery of the Golden Garden. The professor declines at first and after hearing his inspirational talk of solving the greatest puzzles, but Luke then asks the professor if he can go with him as his apprentice. Clark, Doland, and Brenda send Luke off with Layton after some thought about it. Finally better, Arianna thanked Luke for the inspiration he had given her. After all that happened, Luke is given a kiss on the cheek good-bye by Arianna and leaves Misthallery for London with the professor and Emmy.