The Towering Pagoda is rumoured to be the headquarters of Future Layton and The Family. While climbing the Towering Pagoda, Professor Layton, Luke, Flora and Future Luke solve multiple puzzles, including one requiring a strange glasses-type device to be worn. After coming to the top, the crew discover that the person claiming to be Future Layton is indeed Dr. Stahngun, who is in turn revealed to be Dimitri Allen. He explains that the device Layton had worn to complete one of the puzzles stated earlier is actually a memory collector, and he needed the Professor's memory for his time machine research.
The Professor and Co. are then captured in a metal cage. However, the Professor steps out of the shadows, and the Layton who is caught is actually Don Paolo, working together with Professor Layton. This shocks everybody, and foils Dimitri's plan, as he has in fact Don Paolo's memory instead of the Professor's. Then Dimitri challenges the professor to a Puzzle Battle. It is also revealed that Dimitri has captured Prime Minister Bill Hawks. Afterwards, Dimitri escapes, and members of The Familyclosein on the heroes. They eventually escape, but lose track of Dimitri.
While inside the Towering Pagoda, Layton, Luke, and Flora solve many puzzles. On the first floor of the tower there is the puzzle "Eye of the Dragon". On the next floor Layton and co. solve the puzzle "Strange Glasses". Later on, as they go up the tower, the puzzle "Cave Cover-up" stands in the way of Layton and friends. In the mirror room of the tower there is the puzzle "The Mirror Maze". On the top floor, as they enter the final room, Layton must solve the puzzle "The Dragon Bridge".