Layton and Luke are invited to witness a demonstration of a time machine built by Dr. Alain Stahngun, but the experiment goes wrong and Stahngun and Prime Minister Bill Hawks disappear. A week later, with several scientists reported missing, they receive a letter said to be from Luke ten years in the future and follow it to a clock shop in the London back alleys.

Inside, an old couple reveal another time machine disguised as a giant clock. Layton and Luke are sent to a changed, quasi-steampunk London ten years ahead of their time, where they meet Future Luke.

Future Luke explains that Layton has become the head of a mafia-like mob called the Family and taken control of London. After a brief return to the past to search files about an accident that killed Claire, Layton and Luke go back to the future, bringing Flora, Inspector Chelmey, and Barton with them. As they investigate Future Layton’s whereabouts, Luke is reminded that he will soon be moving with his parents.