During Layton and Luke's search for Claudia, Simon is found dead, with a wooden cog found by Matthew at the scene of the crime. Inspector Chelmey comes to investigate the matter, and initially holds Layton and Luke as suspects, but lets them go. He continues to 'investigate' while Layton and Luke search for leads on the Golden Apple.
After Layton and Luke find the key to the tower, they are called to Reinhold Manor, where Chelmey accuses Layton of murdering Simon. He claims the killer, Layton, struck Simon with a vase covered in Layton's fingerprints, but through clever logic and mistakes 'Chelmey' makes, Layton proves his innocence and discovers that Chelmey is really Don Paolo in disguise.
Near the end of the game, it's revealed that Simon, along with everyone else in St. Mystere, is a robot. Because of this, Simon didn't really die. It turns out that Simon simply malfunctioned. During the credits, Bruno is shown repairing Simon, and another scene shows Ramon's surprise at Simon's survival, while Simon wonders what he is talking about.
Even though Simon dies during the course of the game, he still gives the player at least one puzzle. He gives the professor the puzzle "Arc and Line".