Three years before the events in the first game, Professor Layton receives a letter from his old schoolmate Clark Triton. It states that “a mysterious giant shrouded in fog has been laying waste to our houses.” The professor heads to the town of Misthallery to investigate, and is joined by Emmy, his new assistant. What is the meaning of all the destruction, and is it related to the village’s folklore legend of a “specter”? The unfolding story details how Professor Layton and his apprentice, Luke, met.
Professor Layton and the Last Specter follows the structure that has become a staple for the series, in which the player is presented with a succession of puzzles scattered throughout the game world to solve with logic using the touchscreen, with bonus puzzles made available to download on a weekly basis.
In the Japanese and North American releases, the game also includes Professor Layton's London Life, a bonus role-playing game wherein the player’s character lives in Little London with Professor Layton and a number of characters from the series. Players can customize their character with special clothing and collect items and furniture. Some of these help the player’s character to enter certain areas of the city or perform tasks that help out the townspeople.