The manga presents a simplified adaptation of the story and features a number of key changes to the plot. Certain characters, such as Viola, Claves and Falsetto, are absent, and Salsa and March feature only briefly.
The story of the manga contains key differences from the game, though many similarities remain. Among the more notable differences between the manga and the game:
- In the game, Dolce ran an independent pirate ship, while in the manga she works for Count Waltz.
- In the manga, none of the agents who work for Forte die. Some appear more mild-mannered compared to their video game counterpart, save for Fugue.
- In the game, the Cabasa Bridge is destroyed by Tuba. In the manga, it is stated the bridge "collapsed" and the party never attempts to cross it.
- In the game, the party travels to the Mandolin Chruch Grotto and defeats the Root Lurker. In the manga, the noises emanating from underneath the church are simply made by cracks.
- In the manga, there is no mention of Andantino or a rebel group despite Jazz appearing in it.