As with previous Professor Layton games, Unwound Future is an adventure game where the player solves puzzles offered by local citizens to progress the story forward, through dialogue and around 32 minutes of full motion video. The player moves about the game through still images of locations. The player can use the DS touchscreen to tap on non-player characters to start a dialog or to obtain a puzzle, and also can search anywhere on the background for hint coins, with some areas needing to be tapped several times to reveal a secret hint coin or puzzle. Puzzles are brainteasers of many varieties, including visual, math, and logic. There is no time limit to solve puzzles, and the player can get up to 3 hints at a cost of one hint coin each; a new feature in Unwound Future is a "super hint", costing 2 coins, that can only be bought after the other 3 hints have been revealed, but that nearly reveals the puzzle's solution. If the player is correct in solving the puzzle, they gain a number of "Picarats", a form of currency within the game. Guessing the incorrect answer will reduce the number of picarats the player can get on subsequent attempts. Players can visit certain areas in order to play undiscovered or unsolved puzzles that are left behind as the story progresses.

As Layton and Luke are invited to witness a demonstration of a time machine built by Dr. Alain Stahngun, the experiment goes awry, causing the disappearance of Stahngun and the prime minister, Bill Hawks. A week later, as numerous scientists have been reported missing, Layton and Luke receive a letter purporting to be from Luke ten years in the future, leading the two to a quaint clock shop in the London back alleys. Inside, the old couple show the two another time machine in the guise of a giant clock, and they find themselves in a drastically-changed quasi-steam punk London ten years from their present, where they meet the Future Luke. He explains that in this future, Layton has become the head of a mafia-like mob known as the Family and taken control of London, and decides to assist him. After briefly returning to the past to look up some files pertaining to an accident which claimed the life of his girlfriend, Claire, ten years ago, Layton and Luke return to the future London, inadvertently bringing Flora, Inspector Chelmey and his assistant Barton with him. As the group investigates the whereabouts of Future Layton, Luke is reminded that he will soon be moving with his parents.