"Solve the case that brought Professor Layton and Luke together! In the foggy town of Misthallery, the professor investigates rumors of a mythical specter. He soon discovers a link between the specter and a young boy named Luke, who will help him get to the bottom of this baffling mystery..."
The story is of significance, as it details how Professor Layton met Luke Triton and introduces Layton's original assistant Emmy. An additional Adventure game known as London Life will be added along with the main game. This mode will comprise over 100 hours of gameplay. This mode was co-developed by Brownie Brown. Last Specter was released in North America on October 17, 2011. On November 25, 2011, Spectre's Call arrived in Europe. Controversially, the additional RPG game Professor Layton's London Life was not included in the European version, owing to time constraints as to translating it into so many languages.
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.
Once Layton and Emmy arrive at Misthallery, they begin searching for Clark's house. Along the way, they hear rumors of the specter, a witch's mark, and an oracle that can somehow predict the specter's attacks. 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.
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. Layton realizes that Luke was the "oracle" that everyone in town listened to and took refuge to avoid the specter. At first, Layton was doubtful about there being a 'specter' in the town, though Luke insists, so Layton and Emmy continue to look.
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.
But the specter is nowhere to be found, and the trio decides to find the source of the flute music still echoing through the town. After losing the trail around Highyard Arch, Luke mentions a rumor that an ancient flute was sold off at the black market. With their new plan in mind, Layton, Luke and Emmy return to the hotel for the night.
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 finds the Black Raven. Layton gains the Raven's respect by exposing his true identity-he is not one person. All of the children the trio met in the market, who guided them toward the black market, dressed up in the same costume to test Layton and company. The Raven reveals himself as 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. However, no one's been to Mr. Barde's manor in years, because of his daughter, Arianna. Bad things happen to people who speak ill of Arianna, and the townsfolk suspect that Arianna is a cursed witch. With this new information, Layton begins to set his sights on Barde Manor atop Highyard Hill.
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. Once outside, Luke informs Layton and Emmy that Arianna is actually very sick, with not much life left to live. The trio decides to ask around Highyard Hill for information.
Later, they learn that Seamus the gardener is heading down the canal towards the market. The trio follows the trail, hoping that if they can prove that Arianna is not a witch, she would help them solve the mystery. At the market, they hear talk about a boy from Highyard Hill arriving at the market, going on a shopping spree, and completely cleaning out Aunt Taffy's candy supply. With this information, the threesome head back to town.
Upon arriving in town, they learn that the witch's mark has appeared once again, this time in the East District. A candy wrapper found next to the mark confirms Layton's suspicions, and he, Luke and Emmy head back to Barde Manor.
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. It was Tony who created the rumor of the witch's curse and painted the witch's mark on the homes of those who said mean things about 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.
Emmy takes her scooter 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.
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 finally gets a clear glimpse of the "specter". Before Layton can explain, 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 professor realizes-Jakes and his men were immediately on the scene, but Luke didn't alert the townspeople this time. The three escape the interrogation room and leave. Once outside, the group return to their investigation and head back to Highyard Arch to solve one last mystery-the specter's flute.
Arriving at the destroyed arch, Layton realizes how the flute's sound traveled. The old pipe system in Misthallery carried the sound across the town, resulting in the echoing quality of the music. Layton explains this to Emmy and Luke, and then head to the pipe system's origin, Misthallery Lake, to find the specter.
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.
But, as Layton reveals, Loosha is not actually the specter-at least, technically. Loosha was actually protecting Misthallery from the specter, and Arianna was playing the flute to calm Loosha and keep her out of harm's way. Before Arianna can explain, 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.
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". The group heads to Grand Plaza, but Layton has an idea. The three split up, and Layton enters the plaza.
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. Loosha was trying to stop the machine from unearthing the Golden Garden. The "specter" everyone saw was actually Loosha fighting the machine. Behind the thick, manmade fog, the two appeared to be a single entity rampaging through town. However, not only that, the professor then reveals who was behind everything thus far-none other than Doland Noble, the Triton family's faithful butler. But, it would seem that he is not the real Doland at all. Layton explains that the fake Doland kidnapped the real Doland as well as Mrs. Triton, and he sent Emmy to free them. Doland 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 the other 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.
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 with 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, with the help of the Black Ravens, 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 and the professor still wondering who Descole is-and how he knows Layton.
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. Layton realizes why Loosha was fighting Descole in the first place: the air in the Golden Garden, untouched and pure, has properties that may be able to cure Arianna of her illness. Had Descole found the Garden first, that wouldn't be possible. So Loosha opposed Descole all the way, thwarting him long before Layton and Emmy arrived. 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.