Marathon Mode is an additional mode available in Rhythm Thief and the Emperor's Treasure. It allows the player to continue playing a certain type of minigame until they miss three notes. Their score is counted based on how many they manage to hit before getting three Harsh notes. The maximum score is 999, at which point any further notes hit will not count. There are four levels, each of which can be bought in Auban's Shop for 20 medals.
The first level of Marathon Mode is Dance Marathon, and it is available for purchase at the beginning of the game. It contains a medley of various songs in the game, including Phantom Fondue, Battle Diabolique, and Throwdown with Alfred, all put to music where the player must slide in a certain direction to dance or draw a circle to spin, like in the minigame Showtime.
The second level of Marathon Mode is Kick Marathon, which is available after completing Charlie Takes the Field. The music that plays is a combination of the tunes from Charlie Takes the Field and Rematch with Charlie. After 280 kicks, the music restarts. Just like in the two kick minigames, the player must tap to kick in time with the rhythm and slide up when Charlie kicks the ball high into the air.
The third level of Marathon Mode is Samba Marathon. It becomes available after playing Feel the Magic. Like Dance Marathon, Samba Marathon contains a medley of various unrelated songs in the game, such as Samba Carnival, Rhythm Kitchen, Enter the Waiter, and The Last Dance. Like the two samba-themed minigames, the player must press X, A, B, up, left, and down when the corresponding notes appear on the screen.
These are the songs that play in Samba Marathon, in order of appearance. They loop after a score of 999 is reached, returning back to Samba Carnival.
- Samba Carnival
- Bone Appétit
- Fondue to the Rescue
- Hurry Up and Wait
- Restaurant Test
- It's Dog Showtime
- Rhythm Kitchen
- Feel the Magic
- Return of the Faux Phantom R
- Enter the Waiter
- The Last Dance
The fourth and final level of Marathon Mode is Battle Marathon. It combines multiple songs from minigames where Phantom R battles the Chevaliers Diabolique. It begins with only red Chevaliers Diabolique which the player can fend off with the A button, but after 218 notes, blue Chevaliers appear that must be attacked with the B button.
- Kick Marathon introduces quadruple rapid kicks, since Rematch with Charlie only features up to three consecutive rapid kicks.