Professor Layton and Luke first visit the clock shop after receiving a letter from Future Luke with directions. They manage to solve the puzzle on the door of the shop and enter. They are greeted by Spring, who tells them that her husband Cogg will return soon. After Cogg returns, they use the time machine in the back room to travel to Future London. After that, the door of the shop remains locked, so they can no longer enter it.
Later on, Future Luke learns Professor Layton and Luke the secret knock to gain access to the shop again. They make use of the time machine to travel back to the present London so Layton can gather some information from Scotland Yard.
The time machine in the shop is used a third time when the professor and Luke try to go back to the future. Before they can leave, however, Inspector Chelmey, Barton and Flora barge in. Due to limited time, Cogg activates the machine anyway and brings them all to Future London.
In the end, the clock shop is used to evacuate the citizens of Future London back to the real London.
The clock shop houses a few puzzles early on in the game. While waiting for Cogg to arrive, Layton makes a couple of puzzles up. These puzzles are "What's the Time" and "The Odd Clock". Another puzzle must be solved in order to enter the Shop. This puzzle is "The Timepiece".