Following the attacks, it seems like Chief Jakes really has it out for you, so you better hurry with the investigation. Luke says that only Doland knows about his predictions, and that he has no idea where the specter may strike next. From Luke's notes, Layton works out that the specter will strike anywhere between Highyard Arch and the reservoir.
Setting up a trap
Once you get to Highyard Arch, Luke confirms Layton's predictions. He reveals that he can tell where the specter attacks by the water level of the canals. The water level always lowers before a specter attack on that town. Even though Luke is usually in his room, he has his pet mouse Toppy scout out the water levels of the canals for him. Layton wants Luke to keep the prediction from the police this time, as he plans to lay a trap for the specter. Mystery 03 will be solved!
In a candlelit room, Chief Jakes visits a mysterious man and tells him about Layton's investigation. The man does not underestimate Layton and knows he will eventually discover the truth, and begins planning for the inevitable... Meanwhile, back in Highyard Arch, you have to evacuate the area without alerting the police. Luke suggests asking the well-respected Mr. Greppe to evacuate the town. You'll get the Toppy's Secret Episode.
Note that at this point, if you have collected up to 10 mouse badges from the mice around town, you can head to the Crossroads and talk to the officer for a neat little minigame. Move to Paddy's Place where Mr. Greppe is dining and talk to him. Mr. Greppe is initially reluctant, but after some persuasion and solving Puzzle 091, he will agree to help you. You'll get the Undersea Pipes tank for solving the puzzle. Now, you need to head to the black market for the next part of Layton's plans.
As you're going south to the black market, you can take a short detour to Gresenheller U and enter Layton's Office. Talk to Rosa for an easily miss-able Puzzle 090. Back at Misthallery, you don't have to venture deep into the black market to find Crow. He is hanging out at the Market Center, so talk to him to convince him to help you with the trap.
It's nightfall at Highyard Arch. Layton, Emmy and Luke are all waiting for the specter to appear. As predicted, the fog thickens, and the sound of a flute echoes through the area. The specter begins its attack tearing through buildings and roads and knocking down archways. It falls and stares at Layton briefly before continuing down its path of destruction. Layton has figured out who the specter really is, but before he can announce the culprit, Chief Jakes arrives with the local police and arrests all of you!
At the police station, Chief Jakes claims he arrested you for causing the specter attacks. After he leaves, Layton will note how the police were oddly on the scene moments after the specter appeared, despite never being tipped off by Luke's prediction. He thinks this is related to the specter's identity, but has to solve one more mystery to be certain. Layton plots to break out of the police station, just as Chief Jakes makes another visit to the person in the dim room. The mysterious mastermind is quite clever, and predicts Layton will escape from the police station.
Back in the Interrogation Cell, be sure to examine the room thoroughly before leaving. Tap the window above the door repeatedly, the light switch and the cabinet in the corner for Hint Coins. Now check the door for Puzzle 092, which you must solve to leave the cell. In the hallway, go right to trigger Puzzle 093. Solve this puzzle and you're free!
Outside, Layton wishes to visit the locations of specter attacks to see what they have in common. He suggests checking out Highyard Arch first. On your way there, talk to Hans at the Twisted Light for Puzzle 094. At the Grand Plaza, Maggie will give you Puzzle 095 and Otaki-san challenges you with Puzzle 096. Go south from there to reach the Wrecked Arch.
The specter had certainly left a mark on this ruined street, but thankfully no one is hurt. Layton thinks that the specter may be the one causing the thick fog to obscure its appearance. You should investigate the area to find clues. Tap the rusty pipe jutting out of the ground. Seeing it prompts a Eureka moment for Layton, and he has figured out how the specter's flute can be heard.
Puzzle: The mystery of the flute
Q: What did the flute sound like when the specter appeared?
A. It echoed through the town. B. The specter drowned it out. C. It had a jazz-fusion flair.
Q: "How was the music being carried all over town?"
A. An information network. B. Through old pipes. C. Down the canals.
To the flute's source
Now that you know how the flute can be heard across the whole town, there's one spot that is likely to be the source of the flute music: the lake by Barde Manor. All will be made clear once you get to Highyard Hill.