Towards the beginning of the game, going here doesn't accomplish much at all. In the later parts of the game, however, the Thames Arms is gone to many times for many different reasons. The first time Layton and Luke must go is for their confrontation with Future Layton, however he was nowhere to be seen. Later, the Thames Arms is where Layton and Future Luke talk about where Dimitri is hiding after he escaped the Towering Pagoda. Almost the entire twelfth chapter is also spent inside the Thames Arms solving the mystery surrounding Future London.
Luke and Layton also meet up with Barton a couple of times here. He is peeking in the window, most likely trying to see if the restaurant is closed or not.
Towards the beginning of the game, going here doesn't accomplish much at all. Future Luke later wants to go to the restaurant to discuss how the group can infiltrate the base just as they discussed at the restaurant in the arcade.
Layton and his friends head into the Thames Arms after infiltrating and escaping the Research Facility across the River Thames. Future Luke greets Layton and asks him to enter the building. Inside were Inspector Chelmey, Barton, Celeste, Future Luke, and the Barkeep, as well as Layton's crew of Luke, Don Paolo, Flora, and himself. Upon their entrance, they start to eat and think of a way to stop the family and what Dimitri's plans are, as well as finding Dimitri in the first place! Layton then says he has much to say about Future London and what is really going on here. He begins by telling all of the people, gathered in the room, that the bartender is, in fact, non other than Dimitri Allen in disguise. This begins the third and final Puzzle Battle.
Dimitri is trying to escape the Thames Arms unharmed as he knows where all of the explosives he has hidden away are. If anyone moves too close to these explosives, Dimitri will detonate them or they will detonate themselves. Layton quickly realizes a flaw in this plan. By using a clue that Dimitri gave him, he managed to find the placement of all of the bombs in the room. Dimitri tells him that he can't do much with that knowledge, but Layton thinks otherwise. When upside down, marked with the location of the bombs as well, the piece of paper reads, "LIE". This infers that what Dimitri has been saying thus far has been one huge lie, there are no explosives at all. With his escape plan foiled, Dimitri has no other choice but to stay for his interrogation by Professor Layton.
Dimitri and Layton begin their long conversation regarding what Dimitri's goal's and intentions were Layton and Dimitri. Dimitri reveals his plan, starting with what happened Ten years ago. Bill Hawks and Dimitri, along with their assistant, Claire, were working on a Time Machine. He also mentioned that he had loved Claire, just as Paul and Layton did, but even though Claire did not return the feelings, Dimitri never stopped loving her. Bill and Dimitri began to fight each other for who the first human test subject should be. Bill also though Claire was a good enough candidate for the position. Dimitri opposed this idea, indefinitely. Around this time, he also noticed a flaw in the Time Machine's design, one that would cause a major disaster if left unfixed. In order to fix it, he insisted Bill to postpone the experiment, but Bill didn't care as he was secretly offered fame and glory for this experiment. By the time, Dimitri got to the building, the experiment was already taking place. All Dimitri wanted to do, was go back in time and save Claire from her fate. Layton then tells him that it is impossible to rewrite history and Dimitri goes into a state of denial. Layton also begins to say of who is the true mastermind behind all that has happened here thus far.
Layton:Someone here masterminded a scheme even more awful than yours, Dimitri. And that person is there!
Clive:Hmph! I think you're mistaken, Professor.
Layton:No, there's no mistake here, 'Future Luke'. Or should I call you... Clive?
Professor Layton reveals that the true villain is Future Luke. This so-called Future Luke takes off his hat and laughs maniacally begins to say what he has been planning, but thinks of a much easier way to just show them all. Clive, who had been posing as Future Luke, grabs Flora and takes off in haste. Layton and crew follow him outside, but Clive has already began his escape to the lighthouse via motorboat. Upon Clive's arrival at the island, a large tremor occurs. Layton tells all in the area to move to higher ground and then moves himself. The lighthouse begins to rise up, but then an even larger tremor occurs. Clive's dormant Mobile Fortress rises up and begins to destroy parts of Future London. Layton and crew think of a plan of action in order to enter the massive war machine. On of the legs of the fortress crushes down from the fortress. Paul tells them that he has a way to enter the fortress, but it won't be easy. Layton and Luke head up the hill and find a replica of the Laytonmobile. Here, they enter and begin to drive the car. Chelmey thinks this is madness and begins to warn them. Nevertheless, Layton drives and eventually makes enough airtime and lands on a platform aboard the lower levels of the fortress, and then uses some of the outside paths of the machine to climb up to the upper levels. In the ending credits, Dimitri, Chelmey, and Paul are observing the flying machine Paul invented and Celeste flies off with it to the Mobile Fortress.
The Thames Arms remains destroyed for the rest of the game. It acts as the landing site for Don Paolo's flying machine when the player returns to Future London during or after chapter thirteen.
The Thames Arms does not give any puzzles on its own, but the player receives multiple puzzles here. The puzzle "Diced Dates" is given by the Barkeep. The third and final Puzzle Battle also takes place here.
The area around the Thames Arms houses a few puzzles as well, such as "A Zero-Sum Game" (by the entrance to the tunnel), "Paving the Garden" (in the shady grove to the east) and "Time Cards" (in the water outside the building).
The Thames Arms could be a wild reference to The King's Arms Restaurant, as it is located in a very similar spot and is a similar building.
During the cut-scene when the Mobile Fortress rises, everyone but Dimitri is seen outside, but Dimitri is still alive as proved by being in the epilogue and witnessing Don Paolo's flying apparatus take flight.