The professor's old friend, Dr. Andrew Schrader, wrote to Professor Layton, claiming that he has come into possession of the box. He believed he was close to solving the mystery, but he could not contain his curiosity, and that he planned to open the box before finishing his research, and that if anything happened to him, he wanted Layton to finish his work. Layton and Luke, worried, drove to Dr. Schrader's flat, only to find him dead on the floor, and the box gone.
They decided to take a trip on The Molentary Express, finding a ticket in Schrader's pocket. Here, they met up with Flora, and arrived at a little village called Dropstone, which was celebrating its 50th anniversary. As they explored the village, Layton furthered his investigation, believing that this town was deeply connected to the Elysian Box. After a lot of searching, they talked with Mr. Anderson, the most influential man in Dropstone, and discovered that his late mother-in-law, Sophia, had founded the village, and had also searched for the box as well, but had failed.
The trio boarded the train again, and sneaked into the deluxe car. Here, Layton and crew were drugged into a deep sleep by the train conductor, Sammy Thunder. As they slept, their carriage secretly switched track, and headed with another train to the phantom town of Folsense.
As they searched the large city, more clues and mysteries began to emerge. After searching the mines to the north, Layton was confronted by Barton, a bobby of Inspector Chelmey. He told them to go back to the hotel in order to discuss the murder of Dr. Schrader. In the hotel, they discover that Flora was really Don Paolo in disguise. In Don's haste to escape, he accidentally dropped the box. Layton quickly noticed, and so did Mr. Beluga. Beluga told Layton that it belongs to him, being a son of the late Duke, but Krantz said otherwise. Since Beluga left Folsense long ago, changing his name and forgetting the past, he was disowned by his father, and no longer had claim to the Herzen family's treasures. Layton and Luke brought the box to their room and opened it, only to find it empty. Layton realized a deeper mystery. and the two proceeded to Herzen Castle.
After searching more, they headed up to Herzen Castle, despite the people's warnings about a vampire who lived there. Instead of a vampire, they discovered the Duke of Folsense, a young man called Anton, who appeared not to have aged in the last 50 years. Anton gave them a warm welcome, and allowed them to stay the night. Later, Anton tied them up in the cellar. Layton and Luke easily freed themselves, and found that the castle was built over an excavation pit emitting a strange fume.
They found Katia, daughter of Mr. Anderson, and she implored for them to leave the castle. But Anton caught them sneaking out. On sight of Katia, Anton became bewildered, since she was almost identical to his sweetheart Sophia, who left him years ago. Anton challenged Layton to a swordfight, but quickly deteriorated in doing so. With help from Katia, Layton explained the mystery to Anton.
50 years ago, the thriving mining town of Folsense was struck by a deadly disease caused by the fumes in the mines. Most of the town's people evacuated, including Anton's fiancée, Sophia. Sophia had left because she was pregnant, and wanted to protect their child. Anton thought she had left to be with another man. Alone and affected by the gas, Anton continued to imagine the town in its former glory, the Folsense of fifty years ago. Katia is Anton's granddaughter, and she had come to Folsense on her dead grandmother's wishes; to meet Anton, and bring him home to Dropstone.
Anton refused to hear the truth; Sophia's death was too much for him. He started swinging madly at anything, almost killing Layton, in his sight with his sword, and in doing so, dropped a truly massive chandelier. It caused the castle to collapse when it falls with great force. They all managed to escape.
The debris of the castle plugs the hole in which the fumes were coming from, and the illusion of Folsense disappears, revealing a long-abandoned, neglected town. Anton now shows his true aged form and is happy to have delight in life again: Katia. Anton explains that he had the box made as a gift for Sophia when they were together, and sent with a letter inside when she left.
"The Sun rises when you and I meet and when the wind blows, you will know my heart."
-The words to open the Elysian Box
Anton then shows Luke how to open the box in a special way, and reveals a letter from Sophia, written before her death. In the letter, Sophia explains why she had left and that she wishes for Anton to be with their granddaughter. Anton, tears in his eyes, asks if Sophia is listening, then asks that she forgive him for keeping her waiting a little while longer, as he has to get to know Katia first. In the end, the most powerful message from the box was not one of terror; one of love.