The Mobile Fortress is the fortress that Clive reveals as his main reason for kidnapping the scientists. After Professor Layton uncovers the mysteries of Future London and Future Luke, Clive snatches Flora and brings her with him to the Fortress. Layton and Luke board it driving off a hill and using it as a ramp in the Laytonmobile.
The Mobile Fortress rises up from the River Thames, its top being the already suspicious lighthouse. Layton and Luke found out that Flora was being kept in the ventillation room in a glass cage. But before that they confront Lockjaw inside the fortress. After saving Flora; Layton, Luke and Flora went to confront Clive in the surveillance room. However, Fisheye, another of Clive's minions, bocks the path. Soon after that Layton, Luke and Flora go up the stairs to the surveillance room. Then they confront Clive aboard his 'Fortress of Madness'.
Clive temporarily traps them by making the floor start to fall apart. Then the trio bump into Celeste who leads them to the generator room where Clive is keeping Bill Hawks hostage. They try to save him but this causes the fortress to start destroying itself. It was destroyed after Layton and Celeste wired up a pocket watch to the generator in lieu of the prime minister.
Clive gets knocked unconscious by a falling wire shortly after he realizes this. Celeste sees this while Layton and co. are flying off and goes to save him. Layton drops the others to safety and goes back for Celeste and Clive. The watch could only go without winding for 10 minutes, and when it stopped, the Fortress exploded as it fell back into the cavern of Future London.
The Mobile Fortress consists of multiple floors with rooms, all reachable by the single elevator in the center. Some of the Rooms/Floors can only be reached after a certain puzzle has been solved.
This is the room Clive flees off to after confronting Professor Layton. It is the highest room of the fortress and can be found all the way at the top. As the name suggests, this room is able to control the entire fortress, including the movement and canon fire. This location is not visited in the game, but can be seen in some of the in-game videos.
The Surveillance Room can be found directly under the Control Room. It has a lot of monitors which display the entire fortress. Clive was hiding here until Layton confronts him. He also set up a trap for Layton and built an escape route to the Control Room into the floor.
The Surveillance Floor can only be reached by the elevator after solving a Puzzle.
This is where Flora was kept captive after Clive abducted her. The Ventilation Floor can only be reached after solving a puzzle in the elevator.
The tower base serves as the entrance for the fortress. The Layton mobile stood before the door when Layton and Luke were exploring the fortress. They (after joining with Celeste and Bill Hawks) also manage to escape through here when the fortress began destroying itself.
The generator provides the power needed by the entire fortress. It is located all the way at the bottom of the fortress, under the tower base.
The generator was originally connected to Bill Hawks' chest and was programmed to explode if his heart beat stopped. Layton manages to connect and old watch to the system instead, allowing them to free Bill Hawks. They then switch around some gears and reverse the energy flow, causing the fortress to start destroying itself.
Spoilers end here
Within the Mobile Fortress, many puzzles are found. All of the puzzles solved in the Mobile Fortress are Storyline puzzles. These puzzles are given by Clive and his minions primarily. The first puzzle solved for the Mobile Fortress is "Scrutinized Screws" in order to enter the structure. The next is "Swap to Unlock" outside of the fortress. Afterward, the puzzle "A Cryptic Combo" is solved to enter the elevator. Next is the puzzle "Arrow Flow". This opens Flora's sealed prison. After that Lockjaw gives Layton the puzzle "Password Pieces". Next, Fisheye is found and gives the puzzle "Cat's-Eye View". Clive, later, gives the puzzle "The Final Tile". Using the monitors in here the puzzle "Connect the Bots" is given. Then Layton and co. head down into the generator. The puzzles here are "Ten-Step Solution" and "A Real Heart Swapper". Next enters the ending sequence.
The ending of the Unwound Future happens by selecting the generator another time. This gives the puzzle "Reverse Rotation". Then Layton and co. flee the fortress. This enters the puzzle "Block Blockade" when Layton must escape in his car. Afterwards "The Final Puzzle" is solved after the Ending Credits roll.
The Mobile Fortress
Mobile Fortress (Live)