Memories of Marl Kingdom, unlike the earlier games in the series, consists of six separate chapters, each of which features different characters from the Rhapsody series. The chapters take place in various times before or after the stories of A Musical Adventure and Ballad of the Little Princess. These chapters often address unanswered questions from the earlier games, or provide additional insight into the characters.

Chapter 1: The first chapter is set early in Cornet's adventure in A Musical Adventure and takes place after Ferdinand has been turned to stone. Cornet, Kururu, and Etoile get lost in a forest and end up in a town full of anthropomorphic mushrooms. There, they decide to find a young girl's missing mother.

Chapter 2: The second chapter takes place four years after Ballad of the Little Princess. Kururu, now sixteen, has decided to marry Cello. In order to get her father to accept Cello as a suitable husband, Kururu has to win the upcoming Miss Marl Kingdom competition. This serves as an epilogue to Little Princess. In this chapter, it is heavily implied that Kururu and Cello will eventually be the parents of Homard from La Pucelle: Tactics.

Chapter 3: The third adventure is not firmly established anywhere on the series timeline. The Nyankos of the Marjoly Family have gone missing, and the four women set out to find why they have disappeared.

Chapter 4: The fourth chapter takes place immediately before the events in Ballad of the Little Princess. Pekonyan, a servant of the Akurjo Family, is in love with Pokonyan, a Nyanko for the Marjoly Family. Pekonyan is distraught when she realizes that the Akurjo Family is going to war with the Marjoly Family, and decides to assassinate Akurjo before this happens.

Chapter 5: The fifth and longest chapter in the game takes place thousands of years before A Musical Adventure and, due to its length, is the only chapter in the game to be broken into multiple sub-chapters. This chapter follows Cherie's life from start to finish, from the last days of the Ancient civilization, to the birth of Cornet, to Cherie's death. This is the second bonus chapter to be included in the DS remake of A Musical Adventure.

Chapter 6: The sixth chapter is a bonus boss rush event. In this chapter, every single playable character from every chapter is brought together, regardless of when or where their stories take place, to defeat the Dark Lord.