The gameplay is similar to its predecessor, and the first Layton game for 3DS, but this game includes more dynamic and action sequences, and not just through the cinematics, some of which require puzzle-solving in real-time (i.e. puzzle-fight mini-game trying to shoot down enemy missiles and drones launched at your airship). Hunting for hint coins is just as before, but there are many animated features on actual location sets which was not used in the previous game (i.e. you click on a water hose which starts sprinkling around and tosses something off which reveals a hint coin). There are new and recurring characters in the story, and almost all of them will have some puzzle to offer in a typical Layton sense.
Layton's journal, list of mysteries, unlockable episodes that show sliced events with other characters, and collectable items are unchanged. However, mini-games and additional items are all new. These include: