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In the opening sequence to the game, Professor Layton and Luke are having a conversation while aboard a bus bound for Midland Road. Luke flashes back, remembering an important event from about a week ago. It was a large presentation of, what was claimed to be, the first working time machine, created by one Dr. Alain Stahngun. At the presentation, Stahngun begins to explain the use and procedure of the machine to the crowd. Among this crowd are Layton, Inspector Chelmey, and Prime Minister Bill Hawks.

Dr. Stahngun asks Bill for assistance in a test run of the machine. His wife, Caroline, quickly tells him not to go, but Bill refuses. Stahngun tells him he should give a simple address before proceeding. Bill agrees and he then begins talking. In his speech, he says that time has eluded humans, but now, with this great innovation of science, time itself has been grasped.

After his speech ends, Dr. Stahngun asks Bill to help with the demonstration. Caroline yells at Bill, telling him to stop, Bill once again refusing. Bill enters the machine, unaware of what was to happen next. Stahngun pulls the lever and closes the door. The machine spontaneously explodes, leaving rubble behind with no trace of Dr. Stahngun and his assistants nor Bill. Layton and Chelmey investigate the case and begin to wonder what the fate of London is without the prime minister.

Much later in the game, atop the Towering Pagoda in the future London, Layton and crew confront the future Layton in his office. Layton and Future Layton begin to engage in a battle of wits. In the confusion of their battle, future Layton is proven to be an imposter. However, Layton, Luke, and the rest are trapped in a cage and the future Layton takes off his disguise. Dimitri Allen, a scientist who worked in the field of time travel, turns out to be the villain. He activates a hidden door, revealing that he has indeed kidnapped Bill Hawks for personal reason. Suddenly the real Professor Layton enters and Don Paolo (inside the cage, disguised as Layton) takes his mask off. Layton saves the crew, but Bostro comes and saves Dimitri, and Dimitri takes Bill along with him. Bill isn't seen again, until the final chapter.

When Layton finally tracks Dimitri down and finds him to be the barkeeper at the Thames Arms, Dimitri reveals everything that he is trying to gain from kidnapping Bill. Dimitri has once worked with Bill at the Institute of Polydimensional Research. However, there was an event the split the two apart. Claire, their lab assistant and Layton's girlfriend at the time, was tasked by Bill to be the first human test subject for the machine. Dimitri refused the gesture as he had fallen in love with Claire.

Dimitri and Bill argued, as Dimitri had found a flaw in the machine, but Bill was given a deal by a shady corporation. The corporation had made a deal with Bill to sell thepower source behind the time machine, and all he was required to do to seal the deal was test-run it successfully. Claire and Bill then decided to test the machine. However, upon begining the test, the flaw that Dimitri pointed out was right, and the machine exploded violently, destroying a near-by apartment building as well as the building for the field test.

Dimitri quickly rushed to the scene and many other people were there as well, including Layton. Upon inspecting the scene, Dimitri saw Claire, killed by the blast, lying on the ground. The area was cleaned out and Dimitri had lost both the love of his life, and his entire life's work.

Dimitri explains why he had done everything he had done, how it was all for Claire, but Layton told him that he shouldn't have done it and nothing will excuse the kidnappings of the all the scientists and the lies he fed them. Afterward, Layton then tells him, that he is even a pawn in this twisted game.

The Mobile FortressEdit

Layton points to the true villain, the future Luke. The Luke of the future reveals his true name, Clive and tells all in the room he is through with explanations. Upon this accusation, Clive takes his cap off, and rushes out of the building, laughing. He takes a motorboat, and rushes off to the lighthouse. The ground begins to quake and the horrific and deadly nobile fortress begins to rise. Layton and Luke use the modified Laytonmobile to scale the fortress and make their way to the top. Inside, they find Flora, who had been kidnapped by Clive. With Flora in tow, the group go in search for a way to stop Clive.

They manage to find him in the highest chamber of the fortress, but then Clive escapes and tells them that they cannot win this fight. Clive's fortress rises up into the actual London and begins terrorizing the town. Layton and crew reach the lower levels and find the Generator room of the fortress. Upon a closer inspection, they find Bill Hawks trapped inside. The only way to open the generator and stop the fortress is to remove Bill, but once Bill leaves the seat, he dies.

Layton quickly thinks of a way to stop this madness. Using the pocket watch given by Celeste, Celeste points out he will have to exchange the pocket watch and the ticking of Bill's heartneat in move, or the switch will fail. In doing so, he saves Bill's life, and then he reverses the flow in the generator, causing the fortress to start destroying itself. The group then exit the fortress. Using the Laytonmobile's new flying mechanism, installed by Don Paolo, Layton and the rest of the gang fly out of the fortress, landing safely in the streets of London. After the generator begins to slow down, Clive's fortress falls back into the future London, and explodes.

Along the River Thames, Layton, Clive, Inspector Chelmey, Dimitri, and Celeste begin to talk about the events that have transpired. Clive is taken away by police and Bill Hawks makes a comment on how criminals are just the worst kind of people. Chelmey then remarks about how it isn't just criminals. Bill and the rest leave, leaving Layton, Dimitri, and Claire to discuss their plans for the future now that London is once again saved.