Hidden Door Secret Episode 1
In the game's Top Secret menu, there is a section called The Hidden Door. One of its options can only be unlocked by using a 3DS system-unique password found in the Hidden Door section of Professor Layton and the Last Specter. It gives you access to a bonus conversation between the cast, as well as a brief quiz about what happened in the previous game.
Hidden Door Secret Episode 2
In the game's Top Secret menu, there is a section called The Hidden Door. One of its options can only be unlocked by using a 3DS system-unique password found in the Hidden Door section of Professor Layton and the Azran Legacy. It gives you access to a bonus conversation between the cast, and foreshadows events in the Azran Legacy.
Layton's Challenges
Layton's challenges are the hardest puzzles in the game. They are found under the bonuses section. Each one has a different way of being unlocked.
The Puzzle Keeper's House - Solve 147 puzzles.
The Reunion House - Beat the game.
The Ringmaster's House - Complete all ten rabbit plays.
The Shopkeeper's House - Complete all ten shop aisles.
The Toymaker's House - Complete all ten toy robot main stages.
Medal of Completion
If you manage to completely clear all of the aisles in the Shop mini-game, you'll unlock the Medal of Completion in your catalog.
Top Secret Options
Once you acquire enough Picarats and beaten the game, you unlock the following options in the Top Secret section of the Bonuses Menu.
Additional Character Profiles - Solve all 150 puzzles.
Art - Acquire 4,600 Picarats and beat the game.
Character Profiles - Acquire 4,300 Picarats and beat the game.
Character Voices - Acquire 5,200 Picarats and beat the game.
Movies - Acquire 5,500 Picarats and beat the game.
Music - Acquire 4,900 Picarats and beat the game.
Toy Robot Hidden Maze
After you've completed all of the Toy Robot stages, you'll unlock the Hidden Maze in the middle of the world map. The Hidden Maze contains an additional set of stages.