Raphael, a normal boy by day, acts as the legendary art thief Phantom R by night. He is well-known for stealing precious paintings and returning them days later, never getting caught. His true motive can be traced back three years prior to the start of the game, where Raphael's father mysteriously disappeared and left him with a strange coin. Raphael found all of the paintings his father had stolen shortly afterward, replacing them with forgeries. As Phantom R, Raphael works to replace his father's forgeries with the original artworks, meanwhile hoping he will someday find his father again.
At the start of the game, Raphael finds a lead in the form of a museum exhibit which is currently displaying a bracelet with the same symbol as that on his father's coin. As Phantom R publicly announces his intention to steal the bracelet, Raphael must deal with the unraveling of a mystery involving a hostile man who claims to be the historical Napoleon, a mysterious girl named Marie who seems to have some connection to him, and the whereabouts of his very own father that may put him in over his head.
Rhythm Thief & the Emperor's Treasure is a mix of adventure and rhythm, following the story of a Parisian mystery. The player can explore various landmarks of Paris during their search for clues in a point-and-click style reminiscent of Professor Layton. Advancing through the plot may involve solving puzzles or, more frequently, completing a mini-game where Raphael must move to the beat. These games may make use of either the stylus or the gyroscope feature of the 3DS; depending on how closely the player has followed the rhythm, a letter rank will be given. Coins can be found throughout the city and used to buy items for use in a mini-game. Optional mini-games may also be found throughout the city, holding references to other SEGA franchises.