Professor Layton and his apprentice Luke boards the Molentary Express, followed by a familiar-looking girl. In their room, Layton reminds Luke of what brought them on to the express, and thus we return to a few days before. A friend of Layton's, Dr. Schrader, has discovered an artifact called the Elysian Box, rumored to kill anyone that opens it. He wrote a letter to Layton just before he is about to open it. Concerned, Professor Layton decides to visit the doctor. You will get a mystery, The Elysian Box.
Visiting Schrader[edit]
Before we can continue onward, we need to find 
Layton's Keys to the Laytonmobile. There will be a short tutorial about interacting with your environment. Check the middle drawer of the desk to find the keys. Now that we have found a key, Layton will give another tutorial about moving between places. Simply press the boot icon and choose the sole option, right. Out in the corridor, try to move right again. Layton will note that we don't know where the doctor currently resides. You will automatically trigger your first puzzle, Puzzle 001!
After solving the puzzle, Layton and Luke will set off to the doctor's home. After arriving at the doctor's residence, Layton will note that Dr. Schrader gave him the details off his apartment in the letter. You will automatically trigger Puzzle 002. Tap on the only person in this location to talk to him. The person, Damon, will explain how hint coins work, and how you can find them. The mailbox he was blocking contains one hint coin. There are many hint coins hidden like that throughout the game, in fact there are three hidden right now! Tap on the top of the doorway, the base of the street lamp and the rightmost bush on the first floor to get 3 more hint coins. After you've got all the hint coins, tap on the door to enter the building.
In this scene are two more hint coins, one at the left window and one at the bottom of the blue cabinet. Before you proceed, it's a good idea to double-check for any hint coins that you've missed, because you won't be able to return to both of these locations. You might also want to save if you're short on time or are afraid you could get stuck, as you won't be able to quite one of the upcoming puzzles. Tap the doors to find that they're locked. Layton will mention that the doctor attached three keys in his letter, but neither of them work after testing. You will automatically start Puzzle 003.
The Doctor's Room[edit]
You will enter the room only to find the doctor's lifeless body and no Elysian Box. There is also a ticket for a luxury railway called the Molentary Express, but there isn't any destination written on it. You will get another mystery, Train Ticket. Layton will inform the police about Dr. Schrader's death.
Inspector Chelmey and his assistant will arrive on the scene. After a bit of mistaken identity and some conversation, Chelmey deduces that the doctor dies from a heart attack after being surprised by the hanging skeleton, but Layton will note that it could be something more sinister. You will automatically trigger Puzzle 004. You cannot quit this puzzle, and you can't save while solving a puzzle, so if you didn't save before entering, you must solve it if you don't want to lose all of your progress.
Layton will find bits of a 
Torn Photo in Dr. Schrader's hand, but can't make anything out of it. You will get two new mysteries, The Torn Photograph and The Box's Disappearance. Following Schrader's death, Layton decides to use the ticket they found to board the Molentary Express, hopefully to find out the whereabouts of the Elysian Box. Thus, we're back to where we left off in the opening cutscene, and so begins the first chapter of our adventure!