Samuel "Sammy" Thunder is the nephew of Mr. Beluga, the owner of the Molentary Express, and the conductor of the train. Sammy breaks his uncle's camera and gives the player the remaining pieces, starting the camera puzzle.
Sammy was accused, and almost arrested, by Inspector Chelmey of stealing the Elysian Box because he was fed up of being ordered around by Beluga, but Layton quickly proved his theory false and pointed out the true person in possession of the box - Don Paolo, disguised as Flora. Grateful to Layton for proving him innocent, Sammy pulled a few strings to have the Herzen Museum opened.
Sammy did all of the footwork in Beluga's plan to find the Elysian Box, and Beluga constantly ordered him around and degraded him. Eventually Sammy could not take it anymore and rebelled against Beluga, causing Beluga to shun Sammy for the remainder of the game.
- Sammy Thunder stars in the puzzles "Sammy's Necklace" as well as "Sammy's Work Week."
- Sammy makes a cameo appearance in Professor Layton and the Eternal Diva in Layton's classroom