Preparing for the meeting[edit]
Talk to Rosetta, one of Layton's students. Then, talk to Smith for Puzzle 047. Enter the university and talk to Delmona for Puzzle 048. He will also mention about a young lady waiting in Layton's office, which Luke assumes is Flora, the girl from the first game.
Enter Layton's office (the middle door) to meet Flora. She isn't too happy that Layton left her behind again after their previous adventure. Talk to Flora again, which will make her go outside briefly. Layton will note that he can't bring Flora on another dangerous adventure, so we had better finish our preparations here before she returns. Layton will instruct Luke to find a notebook in his office. Check Layton's desk for the notebook, then head out of the university.
Outside, talk to Rosetta for Puzzle 049. Check the bus stop, then select 
Scotland Yard to move there. On the bus, Luke will say that his notebook contains notes about an explosion at a physics laboratory. Though few records of the accident remain, Layton thinks there is something connecting it to the explosion of the time machine a week ago.
Scotland Yard[edit]
Once you arrive, check the doors of the closest building to enter. Talk to Colby to trigger Puzzle 050. After that, take the stairs up to Inspector Chelmey's office. Talk to Barton, who will note that Inspector Chelmey left all of a sudden. He quickly returns, however, saying that he wants to talk to Layton about the prime minister's disappearance. Talk to Chelmey at his desk.
Inspector Chelmey lead the investigation of the case. While he says that no one could have survived the explosion, his team couldn't find any traces of the victims. In total, 8 victims disappeared on that day, two of which is Dr. Stahngun and the prime minister. Layton will ask about the files for the previous explosion at the Polydimensional Institute, but Chelmey states that even a high-ranking officer like himself will have difficulty getting the relevant files. However, to get any lead he can find, Inspector Chelmey lets us look at the files. They are in the building's archives and cannot be moved out of there, so we'll have to go down and see it for ourselves.
A past case[edit]
Back at the reception hall, choose to go down the staircase in the back. Talk to Barton, who will let Layton search through the files. Talk to Barton again for Puzzle 051. After doing so, Layton will say that he found the file, and believe that the prime minister is actually alive and trapped in the future. Go back to Chelmey's office and talk to Inspector Chelmey.
Inspector Chelmey recalls investigating the explosion that happened long ago. One of the scientists involved was called Dimitri Allen, but there are also two other scientists implicated. A lab assistant and several tenants of a nearby building died, but somehow the scientists survived. Layton will present the possibility that the prime minister is currently held in the future, which Chelmey finds hard to believe. Now that we've told him all that we know, exit the building.
Back to the future[edit]
Outside, Layton will say that he has finished his investigation in the present, and suggests that we head back to the clock shop. Take the bus to Midland Road. Move forward and talk to Vito for Puzzle 052. Move forward again to trigger a short conversation. Luke will be worried about travelling through time, while Layton has concerns about what could happen when they return to the future. He decides to leave Luke behind, but Luke insists on following Layton.