When Professor Layton and Luke first enter the tower, the ground below them collapses, and they fall through into the basement. It is in here that Bruno repairs the robot residents of St. Mystere, which causes the rumbling that annoys them. He tells them the truth of the villagers, but urges the two to find out the truth of the Golden Apple for themselves by climbing the tower.
When Professor Layton and Luke reach the top of the tower, they find a beautifully kept cottage. The player then has the choice of entering the cottage, or heading back down to the village to explore more. If the player picks the first option, they are met with the final cutscenes of the game.
Professor Layton and Luke come face-to-face with the mysterious girl that was observing them. She removes her shawl and glasses to reveal herself as Flora Reinhold, the baron's missing daughter. Luke is shocked at this, and Professor Layton explains that she is the Golden Apple everyone had searched for.
Realization is short-lived, as Don Paolo is seen hovering around the tower in an armed flying contraption, again trying to kill Professor Layton and Luke. The three try to use the stairs to evacuate the tower, but a gap in the staircase created by the destruction is only crossed by Luke, who manages to leap on the rubble to the other end. Professor Layton tells him to go on ahead, and he and Flora climb back up the tower.
Professor Layton fashions a makeshift glider and flies out with Flora in tow. Don Paolo draws closer to them, but Layton swerves the glider out of the way, damaging something in Don Paolo's contraption in the process. The villain drops a canvas bag holding Simon, and swears his revenge as Professor Layton and Flora fly to safety. Shortly afterward the player watches the tower crumble to the ground as the sun rises in the early morning.
In the credits, Don Paolo is seen walking out after the contraption crashes and his clothes are torn.